| Next changeset 1:6a76b60e05f5 (2019-10-16) |
|
Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 |
|
added:
README.md README.rst filter.xml macros.xml test-data/krumsiek11.h5ad test-data/krumsiek11.loom test-data/krumsiek11_counts_per_cell test-data/paul15_subsample.h5ad test-data/pbmc68k_reduced.h5ad test-data/pl.clustermap.krumsiek11.png test-data/pl.diffmap.neighbors_gauss_braycurtis.recipe_weinreb17.paul15_subsampl.png test-data/pl.diffmap.neighbors_gauss_braycurtis.recipe_weinreb17.paul15_subsample.png test-data/pl.dotplot.krumsiek11.png test-data/pl.dpt_timeseries.dpt.diffmap.neighbors_gauss_braycurtis.recipe_weinreb17.paul15_subsample.png test-data/pl.heatmap.krumsiek11.png test-data/pl.highest_expr_genes.filter_genes_dispersion.krumsiek11-seurat.png test-data/pl.matrixplot.krumsiek11.png test-data/pl.paga.paul15_gauss_braycurtis.png test-data/pl.pca.pbmc68k_reduced.CD3D_CD79A_components_2d.pdf test-data/pl.pca_loadings.pp.pca.krumsiek11.png test-data/pl.pca_overview.pp.pca.krumsiek11.png test-data/pl.pca_variance_ratio.pp.pca.krumsiek11.png test-data/pl.scatter.krumsiek11.png test-data/pl.scatter.pca.krumsiek11.png test-data/pl.tsne.krumsiek11.png test-data/pl.umap.neighbors_umap_euclidean.recipe_weinreb17.paul15_subsample.png test-data/pl.violin.pbmc68k_reduced_custom.png test-data/pp.filter_cells.krumsiek11-min_counts.h5ad test-data/pp.filter_cells.krumsiek11-min_counts.loom test-data/pp.filter_cells.number_per_cell.krumsiek11-max_genes.tabular test-data/pp.filter_genes.krumsiek11-min_counts.h5ad test-data/pp.filter_genes.number_per_gene.krumsiek11-min_counts.tabular test-data/pp.filter_genes.number_per_gene.pbmc68k_reduced-max_cells.tabular test-data/pp.filter_genes_dispersion.krumsiek11-seurat.h5ad test-data/pp.filter_genes_dispersion.per_gene.krumsiek11-cell_ranger.tabular test-data/pp.filter_genes_dispersion.per_gene.krumsiek11-seurat.tabular test-data/pp.log1p.krumsiek11.h5ad test-data/pp.neighbors_gauss_braycurtis.recipe_weinreb17.paul15_subsample.h5ad test-data/pp.neighbors_umap_euclidean.recipe_weinreb17.paul15_subsample.h5ad test-data/pp.normalize_per_cell.krumsiek11.h5ad test-data/pp.normalize_per_cell.obs.krumsiek11.tabular test-data/pp.pca.krumsiek11.h5ad test-data/pp.pca.krumsiek11_chunk.h5ad test-data/pp.pca.variance.krumsiek11.tabular test-data/pp.recipe_seurat.recipe_zheng17.h5ad test-data/pp.recipe_weinreb17.paul15_subsample.h5ad test-data/pp.recipe_zheng17.random-randint.h5ad test-data/pp.regress_out.krumsiek11.h5ad test-data/pp.scale.krumsiek11.h5ad test-data/pp.scale_max_value.krumsiek11.h5ad test-data/pp.sqrt.krumsiek11.h5ad test-data/pp.subsample.krumsiek11_fraction.h5ad test-data/pp.subsample.krumsiek11_n_obs.h5ad test-data/random-randint.h5ad test-data/random.h5ad test-data/tl.diffmap.neighbors_gauss_braycurtis.recipe_weinreb17.paul15_subsample.X_diffmap.tabular test-data/tl.diffmap.neighbors_gauss_braycurtis.recipe_weinreb17.paul15_subsample.h5ad test-data/tl.dpt.diffmap.neighbors_gauss_braycurtis.recipe_weinreb17.paul15_subsample.h5ad test-data/tl.dpt.diffmap.neighbors_gauss_braycurtis.recipe_weinreb17.paul15_subsample.obs.tabular test-data/tl.dpt.neighbors.paul15_gauss_braycurtis.obs.tabular test-data/tl.louvain.neighbors_gauss_braycurtis.recipe_weinreb17.paul15_subsample.h5ad test-data/tl.paga.neighbors_gauss_braycurtis.recipe_weinreb17.paul15_subsample.h5ad test-data/tl.pca.krumsiek11.h5ad test-data/tl.pca.variance_ratio.krumsiek11.tabular test-data/tl.rank_genes_groups.krumsiek11.h5ad test-data/tl.score_genes.krumsiek11.h5ad test-data/tl.score_genes.krumsiek11.obs.tabular test-data/tl.score_genes_cell_cycle.krumsiek11.h5ad test-data/tl.score_genes_cell_cycle.krumsiek11.obs.tabular test-data/tl.tsne.krumsiek11.h5ad test-data/tl.tsne.krumsiek11_X_tsne.tabular test-data/tl.umap.neighbors_umap_euclidean.recipe_weinreb17.paul15_subsample.h5ad |
| b |
| diff -r 000000000000 -r 6ea5a05a260a README.md --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/README.md Mon Mar 04 10:15:02 2019 -0500 |
| [ |
| @@ -0,0 +1,138 @@ +Scanpy +====== + +## Classification of methods into steps + +Steps: + +1. Filtering + + Methods | Description + --- | --- + `pp.filter_cells` | Filter cell outliers based on counts and numbers of genes expressed. + `pp.filter_genes` | Filter genes based on number of cells or counts. + `pp.filter_genes_dispersion` | Extract highly variable genes + `pp.highly_variable_genes` | Extract highly variable genes + `pp.subsample` | Subsample to a fraction of the number of observations + `queries.gene_coordinates` | (Could not find...) + `queries.mitochondrial_genes` | Retrieves Mitochondrial gene symbols for specific organism through BioMart for filtering + +2. Quality Plots + + These are in-between stages used to measure the effectiveness of a Filtering/Normalisation/Conf.Removal stage either after processing or prior to. + + Methods | Description | Notes + --- | --- | --- + `pp.calculate_qc_metrics` | Calculate quality control metrics + `pl.violin` | violin plot of features, lib. size, or subsets of. + `pl.stacked_violin` | Same as above but for multiple series of features or cells + +3. Normalization + + Methods | Description + --- | --- + `pp.normalize_per_cell` | Normalize total counts per cell + `pp.recipe_zheng17` | Normalization and filtering as of [Zheng17] + `pp.recipe_weinreb17` | Normalization and filtering as of [Weinreb17] + `pp.recipe_seurat` | Normalization and filtering as of Seurat [Satija15] + `pp.log1p` | Logarithmize the data matrix. + `pp.scale` | Scale data to unit variance and zero mean + `pp.sqrt` | + `pp.downsample_counts` | Downsample counts so that each cell has no more than target_counts + +4. Conf. removal + + Methods | Description + --- | --- + `pp.regress_out` | Regress out unwanted sources of variation + `pp.mnn_correct` | Correct batch effects by matching mutual nearest neighbors + `pp.dca` | Deep count autoencoder to denoise the data + `pp.magic` | Markov Affinity-based Graph Imputation of Cells (MAGIC) API to denoise + `tl.sim` | Simulate dynamic gene expression data [Wittman09] + `pp.calculate_qc_metrics` | Calculate quality control metrics + `tl.score_genes` | Score a set of genes + `tl.score_genes_cell_cycle` | Score cell cycle genes + `tl.cyclone` | Assigns scores and predicted class to observations based on cell-cycle genes [Scialdone15] + `tl.sandbag` | Calculates pairs of genes serving as markers for each cell-cycle phase [Scialdone15] + +5. Clustering and Heatmaps + + Methods | Description + --- | --- + `tl.leiden` | Cluster cells into subgroups [Traag18] [Levine15] + `tl.louvain` | Cluster cells into subgroups [Blondel08] [Levine15] [Traag17] + `tl.pca` | Principal component analysis + `pp.pca` | Principal component analysis (appears to be the same func...) + `tl.diffmap` | Diffusion Maps + `tl.tsne` | t-SNE + `tl.umap` | Embed the neighborhood graph using UMAP + `tl.phate` | PHATE + `pp.neighbors` | Compute a neighborhood graph of observations + `tl.rank_genes_groups` | Rank genes for characterizing groups + `pl.rank_genes_groups` | + `pl.rank_genes_groups_dotplot` | + `pl.rank_genes_groups_heatmap` | + `pl.rank_genes_groups_matrixplot` | + `pl.rank_genes_groups_stacked_violin` | + `pl.rank_genes_groups_violin` | + `pl.matrix_plot` | + `pl.heatmap` | + `pl.highest_expr_genes` | + `pl.diffmap` | + +6. Cluster Inspection and plotting + + Methods that draw out the clusters computed in the previous stage, not heatmap or pseudotime related. + + Methods | Description + --- | --- + `pl.clustermap` | + `pl.phate` | + `pl.dotplot` | + `pl.draw_graph` | (really general purpose, would not implement directly) + `pl.filter_genes_dispersion` | (depreciated for 'highly_variable_genes') + `pl.matrix` | (could not find in API) + `pl.pca` | + `pl.pca_loadings` | + `pl.pca_overview` | + `pl.pca_variance_ratio` | + `pl.ranking` | (not sure what this does...) + `pl.scatter` | ([very general purpose](https://icb-scanpy.readthedocs-hosted.com/en/latest/api/scanpy.api.pl.scatter.html), would not implement directly) + `pl.set_rcParams_defaults` | + `pl.set_rcParams_scanpy` | + `pl.sim` | + `pl.tsne` | + `pl.umap` | + +7. Branch/Between-Cluster Inspection + + Pseudotime analysis, relies on initial clustering. + + Methods | Description + --- | --- + `tl.dpt` | Infer progression of cells through geodesic distance along the graph [Haghverdi16] [Wolf17i] + `pl.dpt_groups_pseudotime` | + `pl.dpt_timeseries` | + `tl.paga_compare_paths` | + `tl.paga_degrees` | + `tl.paga_expression_entropies` | + `tl.paga` | Generate cellular maps of differentiation manifolds with complex topologies [Wolf17i] + `pl.paga` | + `pl.paga_adjacency` | + `pl.paga_compare` | + `pl.paga_path` | + `pl.timeseries` | + `pl.timeseries_as_heatmap` | + `pl.timeseries_subplot` | + + +Methods to sort | Description +--- | --- +`tl.ROC_AUC_analysis` | (could not find in API) +`tl.correlation_matrix` | (could not find in API) +`rtools.mnn_concatenate` | (could not find in API) +`utils.compute_association_matrix_of_groups` | (could not find in API) +`utils.cross_entropy_neighbors_in_rep` | (could not find in API) +`utils.merge_groups` | (could not find in API) +`utils.plot_category_association` | (could not find in API) +`utils.select_groups` | (could not find in API) \ No newline at end of file |
| b |
| diff -r 000000000000 -r 6ea5a05a260a README.rst --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/README.rst Mon Mar 04 10:15:02 2019 -0500 |
| b |
| @@ -0,0 +1,105 @@ +The different methods from Scanpy have been grouped by themes: + +1. Filter in `filter.xml` + - Filter cell outliers based on counts and numbers of genes expressed, using `pp.filter_cells` + - Filter genes based on number of cells or counts, using `pp.filter_genes` + - Extract highly variable genes, using `pp.filter_genes_dispersion` + - `tl.highly_variable_genes` (need to be added) + - Subsample to a fraction of the number of observations, using `pp.subsample` + - `queries.gene_coordinates` (need to be added) + - `queries.mitochondrial_genes` (need to be added) + +2. Normalize in `normalize.xml` + - Normalize total counts per cell, using `pp.normalize_per_cell` + - Normalization and filtering as of Zheng et al. (2017), using `pp.recipe_zheng17` + - Normalization and filtering as of Weinreb et al (2017), using `pp.recipe_weinreb17` + - Normalization and filtering as of Seurat et al (2015), using `pp.recipe_seurat` + - Logarithmize the data matrix, using `pp.log1p` + - Scale data to unit variance and zero mean, using `pp.scale` + - Square root the data matrix, using `pp.sqrt` + - Downsample counts, using `pp.downsample_counts` + +3. Remove confounder in `remove_confounders.xml` + - Regress out unwanted sources of variation, using `pp.regress_out` + - `pp.mnn_correct` (need to be added) + - `pp.mnn_correct` (need to be added) + - `pp.magic` (need to be added) + - `tl.sim` (need to be added) + - `pp.calculate_qc_metrics` (need to be added) + - Score a set of genes, using `tl.score_genes` + - Score cell cycle genes, using `tl.score_genes_cell_cycle` + - `tl.cyclone` (need to be added) + - `tl.andbag` (need to be added) + +4. Cluster and reduce dimension in `cluster_reduce_dimension.xml` + - `tl.leiden` (need to be added) + - Cluster cells into subgroups, using `tl.louvain` + - Computes PCA (principal component analysis) coordinates, loadings and variance decomposition, using `pp.pca` + - Computes PCA (principal component analysis) coordinates, loadings and variance decomposition, using `tl.pca` + - Diffusion Maps, using `tl.diffmap` + - t-distributed stochastic neighborhood embedding (tSNE), using `tl.tsne` + - Embed the neighborhood graph using UMAP, using `tl.umap` + - `tl.phate` (need to be added) + - Compute a neighborhood graph of observations, using `pp.neighbors` + - Rank genes for characterizing groups, using `tl.rank_genes_groups` + +4. Inspect + - `tl.paga_compare_paths` (need to be added) + - `tl.paga_degrees` (need to be added) + - `tl.paga_expression_entropies` (need to be added) + - Generate cellular maps of differentiation manifolds with complex topologies, using `tl.paga` + - Infer progression of cells through geodesic distance along the graph, using `tl.dpt` + +5. Plot + 1. Generic + - Scatter plot along observations or variables axes, using `pl.scatter` + - Heatmap of the expression values of set of genes, using `pl.heatmap` + - Makes a dot plot of the expression values, using `pl.dotplot` + - Violin plot, using `pl.violin` + - `pl.stacked_violin` (need to be added) + - Heatmap of the mean expression values per cluster, using `pl.matrixplot` + - Hierarchically-clustered heatmap, using `pl.clustermap` + - `pl.ranking` + + 2. Preprocessing + - Plot the fraction of counts assigned to each gene over all cells, using `pl.highest_expr_genes` + - Plot dispersions versus means for genes, using `pl.filter_genes_dispersion` + - `pl.highly_variable_genes` (need to be added) + - `pl.calculate_qc_metrics` (need to be added) + + 3. PCA + - Scatter plot in PCA coordinates, using `pl.pca` + - Rank genes according to contributions to PCs, using `pl.pca_loadings` + - Scatter plot in PCA coordinates, using `pl.pca_variance_ratio` + - Plot PCA results, using `pl.pca_overview` + + 4. Embeddings + - Scatter plot in tSNE basis, using `pl.tsne` + - Scatter plot in UMAP basis, using `pl.umap` + - Scatter plot in Diffusion Map basis, using `pl.diffmap` + - `pl.draw_graph` (need to be added) + + 5. Branching trajectories and pseudotime, clustering + - Plot groups and pseudotime, using `pl.dpt_groups_pseudotime` + - Heatmap of pseudotime series, using `pl.dpt_timeseries` + - Plot the abstracted graph through thresholding low-connectivity edges, using `pl.paga` + - `pl.paga_compare` (need to be added) + - `pl.paga_path` (need to be added) + + 6. Marker genes: + - Plot ranking of genes using dotplot plot, using `pl.rank_gene_groups` + - `pl.rank_genes_groups_dotplot` (need to be added) + - `pl.rank_genes_groups_heatmap` (need to be added) + - `pl.rank_genes_groups_matrixplot` (need to be added) + - `pl.rank_genes_groups_stacked_violin` (need to be added) + - `pl.rank_genes_groups_violin` (need to be added) + + 7. Misc + - `pl.phate` (need to be added) + - `pl.matrix` (need to be added) + - `pl.paga_adjacency` (need to be added) + - `pl.timeseries` (need to be added) + - `pl.timeseries_as_heatmap` (need to be added) + - `pl.timeseries_subplot` (need to be added) + + \ No newline at end of file |
| b |
| diff -r 000000000000 -r 6ea5a05a260a filter.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/filter.xml Mon Mar 04 10:15:02 2019 -0500 |
| [ |
| b'@@ -0,0 +1,549 @@\n+<tool id="scanpy_filter" name="Filter with scanpy" version="@galaxy_version@">\n+ <description></description>\n+ <macros>\n+ <import>macros.xml</import>\n+ </macros>\n+ <expand macro="requirements"/>\n+ <expand macro="version_command"/>\n+ <command detect_errors="exit_code"><![CDATA[\n+@CMD@\n+ ]]></command>\n+ <configfiles>\n+ <configfile name="script_file"><![CDATA[\n+@CMD_imports@\n+@CMD_read_inputs@\n+\n+#if $method.method == \'pp.filter_cells\'\n+res = sc.pp.filter_cells(\n+ #if $modify_anndata.modify_anndata == \'true\'\n+ adata,\n+ #else\n+ adata.X,\n+ #end if\n+ #if $method.filter.filter == \'min_counts\'\n+ min_counts=$method.filter.min_counts,\n+ #elif $method.filter.filter == \'max_counts\'\n+ max_counts=$method.filter.max_counts,\n+ #elif $method.filter.filter == \'min_genes\'\n+ min_genes=$method.filter.min_genes,\n+ #elif $method.filter.filter == \'max_genes\'\n+ max_genes=$method.filter.max_genes,\n+ #end if\n+ copy=False)\n+\n+ #if $modify_anndata.modify_anndata == \'true\'\n+df = adata.obs\n+ #else\n+df = pd.DataFrame(data=dict(cell_subset=res[0], number_per_cell=res[1]))\n+ #end if\n+\n+ #if $method.filter.filter == \'min_counts\' or $method.filter.filter == \'max_counts\'\n+df.to_csv(\'$counts_per_cell\', sep=\'\\t\')\n+ #elif $method.filter.filter == \'min_genes\' or $method.filter.filter == \'max_genes\'\n+df.to_csv(\'$genes_per_cell\', sep=\'\\t\')\n+ #end if\n+\n+#elif $method.method == \'pp.filter_genes\'\n+res = sc.pp.filter_genes(\n+ #if $modify_anndata.modify_anndata == \'true\'\n+ adata,\n+ #else\n+ adata.X,\n+ #end if\n+ #if $method.filter.filter == \'min_counts\'\n+ min_counts=$method.filter.min_counts,\n+ #elif $method.filter.filter == \'max_counts\'\n+ max_counts=$method.filter.max_counts,\n+ #elif $method.filter.filter == \'min_cells\'\n+ min_cells=$method.filter.min_cells,\n+ #elif $method.filter.filter == \'max_cells\'\n+ max_cells=$method.filter.max_cells,\n+ #end if\n+ copy=False)\n+\n+ #if $modify_anndata.modify_anndata == \'true\'\n+df = adata.var\n+ #else\n+df = pd.DataFrame(data=dict(gene_subset=res[0], number_per_gene=res[1]))\n+ #end if\n+\n+ #if $method.filter.filter == \'min_counts\' or $method.filter.filter == \'max_counts\'\n+df.to_csv(\'$counts_per_gene\', sep=\'\\t\')\n+ #elif $method.filter.filter == \'min_cells\' or $method.filter.filter == \'max_cells\'\n+df.to_csv(\'$cells_per_gene\', sep=\'\\t\')\n+ #end if\n+\n+#elif $method.method == \'pp.filter_genes_dispersion\'\n+res = sc.pp.filter_genes_dispersion(\n+ #if $modify_anndata.modify_anndata == \'true\'\n+ adata,\n+ #else\n+ adata.X,\n+ #end if\n+ flavor=\'$method.flavor.flavor\',\n+ #if $method.flavor.flavor==\'seurat\'\n+ min_mean=$method.flavor.min_mean,\n+ max_mean=$method.flavor.max_mean,\n+ min_disp=$method.flavor.min_disp,\n+ #if $method.flavor.max_disp\n+ max_disp=$method.flavor.max_disp,\n+ #end if\n+ #else\n+ n_top_genes=$method.flavor.n_top_genes,\n+ #end if\n+ n_bins=$method.n_bins,\n+ log=$method.log,\n+ copy=False)\n+\n+ #if $modify_anndata.modify_anndata == \'true\'\n+adata.var.to_csv(\'$per_gene\', sep=\'\\t\')\n+ #else\n+pd.DataFrame(res).to_csv(\'$per_gene\', sep=\'\\t\')\n+ #end if\n+\n+#elif $method.method == \'pp.subsample\'\n+sc.pp.subsample(\n+ data=adata,\n+ #if $method.type.type == \'fraction\'\n+ fraction=$method.type.fraction,\n+ #else if $method.type.type == \'n_obs\'\n+ n_obs=$method.type.n_obs,\n+ #end if\n+ random_state=$method.random_state,\n+ copy=False)\n+\n+#end if\n+\n+@CMD_anndata_write_modify_outputs@\n+]]></configfile>\n+ </configfiles>\n+ <inputs>\n+ <expand macro="inputs_anndata"/>\n+ <conditional name="method">\n+ <param argument="method" type="select" label="Method used for filtering">\n+ <option value="pp.filter_cells">Filter cell outliers based on counts and numbers of genes expressed, using `pp.filter_cells`</option>\n+ <option value="pp.filter_genes'..b'est>\n+ <test expect_num_outputs="1">\n+ <conditional name="input">\n+ <param name="format" value="h5ad" />\n+ <param name="adata" value="krumsiek11.h5ad" />\n+ </conditional>\n+ <conditional name="method">\n+ <param name="method" value="pp.subsample"/>\n+ <conditional name="type">\n+ <param name="type" value="n_obs" />\n+ <param name="n_obs" value="10"/>\n+ </conditional>\n+ <param name="random_state" value="0"/>\n+ </conditional>\n+ <conditional name="modify_anndata">\n+ <param name="modify_anndata" value="true"/>\n+ <param name="anndata_output_format" value="h5ad" />\n+ </conditional>\n+ <assert_stdout>\n+ <has_text_matching expression="sc.pp.subsample"/>\n+ <has_text_matching expression="n_obs=10"/>\n+ <has_text_matching expression="random_state=0"/>\n+ </assert_stdout>\n+ <output name="anndata_out_h5ad" file="pp.subsample.krumsiek11_n_obs.h5ad" ftype="h5" compare="sim_size"/>\n+ </test>\n+ </tests>\n+ <help><![CDATA[\n+\n+Filter cells outliers based on counts and numbers of genes expressed (`pp.filter_cells`)\n+========================================================================================\n+\n+For instance, only keep cells with at least `min_counts` counts or\n+`min_genes` genes expressed. This is to filter measurement outliers, i.e.,\n+"unreliable" observations.\n+\n+Only provide one of the optional parameters `min_counts`, `min_genes`,\n+`max_counts`, `max_genes` per call.\n+\n+More details on the `scanpy documentation\n+<https://scanpy.readthedocs.io/en/latest/api/scanpy.api.pp.filter_cells.html#scanpy.api.pp.filter_cells>`__\n+\n+Return\n+------\n+\n+number_per_cell : Number per cell (either `n_counts` or `n_genes` per cell)\n+\n+\n+Filter genes based on number of cells or counts (`pp.filter_genes`)\n+===================================================================\n+\n+Keep genes that have at least `min_counts` counts or are expressed in at\n+least `min_cells` cells or have at most `max_counts` counts or are expressed\n+in at most `max_cells` cells.\n+\n+Only provide one of the optional parameters `min_counts`, `min_cells`,\n+`max_counts`, `max_cells` per call.\n+\n+More details on the `scanpy documentation\n+<https://scanpy.readthedocs.io/en/latest/api/scanpy.api.pp.filter_genes.html#scanpy.api.pp.filter_genes>`__\n+\n+Return\n+------\n+\n+number_per_gene : Number per genes (either `n_counts` or `n_genes` per cell)\n+\n+\n+Extract highly variable genes (`pp.filter_genes_dispersion`)\n+============================================================\n+\n+If trying out parameters, pass the data matrix instead of AnnData.\n+\n+Depending on `flavor`, this reproduces the R-implementations of Seurat and Cell Ranger.\n+\n+The normalized dispersion is obtained by scaling with the mean and standard\n+deviation of the dispersions for genes falling into a given bin for mean\n+expression of genes. This means that for each bin of mean expression, highly\n+variable genes are selected.\n+\n+Use `flavor=\'cell_ranger\'` with care and in the same way as in `pp.recipe_zheng17`.\n+\n+More details on the `scanpy documentation\n+<https://scanpy.readthedocs.io/en/latest/api/scanpy.api.pp.filter_genes_dispersion.html#scanpy.api.pp.filter_genes_dispersion>`__\n+\n+Returns\n+-------\n+- The annotated matrix filtered, with the annotations\n+- A table with the means, dispersions, and normalized dispersions per gene, logarithmized when `log` is `True`.\n+\n+\n+Subsample to a fraction of the number of observations (`pp.subsample`)\n+======================================================================\n+\n+More details on the `scanpy documentation\n+<https://scanpy.readthedocs.io/en/latest/api/scanpy.api.pp.subsample.html#scanpy.api.pp.subsample>`__\n+\n+\n+ ]]></help>\n+ <expand macro="citations"/>\n+</tool>\n' |
| b |
| diff -r 000000000000 -r 6ea5a05a260a macros.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macros.xml Mon Mar 04 10:15:02 2019 -0500 |
| [ |
| b'@@ -0,0 +1,1084 @@\n+<macros>\n+ <token name="@version@">1.4</token>\n+ <token name="@galaxy_version@"><![CDATA[@version@+galaxy0]]></token>\n+ <xml name="requirements">\n+ <requirements>\n+ <requirement type="package" version="@version@">scanpy</requirement>\n+ <requirement type="package" version="2.0.17">loompy</requirement>\n+ <yield />\n+ </requirements>\n+ </xml>\n+ <xml name="citations">\n+ <citations>\n+ <citation type="doi">10.1186/s13059-017-1382-0</citation>\n+ </citations>\n+ </xml>\n+ <xml name="version_command">\n+ <version_command><![CDATA[python -c "import scanpy.api as sc;print(\'scanpy version: %s\' % sc.__version__)"]]></version_command>\n+ </xml>\n+ <token name="@CMD@"><![CDATA[\n+cat \'$script_file\' &&\n+python \'$script_file\'\n+ ]]>\n+ </token>\n+ <token name="@CMD_imports@"><![CDATA[\n+import scanpy.api as sc\n+import pandas as pd\n+import numpy as np\n+ ]]>\n+ </token>\n+ <xml name="inputs_anndata">\n+ <conditional name="input">\n+ <param name="format" type="select" label="Format for the annotated data matrix">\n+ <option value="loom">loom</option>\n+ <option value="h5ad">h5ad-formatted hdf5 (anndata)</option>\n+ </param>\n+ <when value="loom">\n+ <param name="adata" type="data" format="loom" label="Annotated data matrix"/>\n+ <param name="sparse" type="boolean" truevalue="True" falsevalue="False" checked="true" label="Is the data matrix to read sparse?"/>\n+ <param name="cleanup" type="boolean" truevalue="True" falsevalue="False" checked="false" label="Cleanup?"/>\n+ <param name="x_name" type="text" value="spliced" label="X_name"/>\n+ <param name="obs_names" type="text" value="CellID" label="obs_names"/>\n+ <param name="var_names" type="text" value="Gene" label="var_names"/>\n+ </when>\n+ <when value="h5ad">\n+ <param name="adata" type="data" format="h5" label="Annotated data matrix"/>\n+ </when>\n+ </conditional>\n+ </xml>\n+ <token name="@CMD_read_inputs@"><![CDATA[\n+#if $input.format == \'loom\'\n+adata = sc.read_loom(\n+ \'$input.adata\',\n+ sparse=$input.sparse,\n+ cleanup=$input.cleanup,\n+ X_name=\'$input.x_name\',\n+ obs_names=\'$input.obs_names\',\n+ var_names=\'$input.var_names\')\n+#else if $input.format == \'h5ad\'\n+adata = sc.read_h5ad(\'$input.adata\')\n+#end if\n+]]>\n+ </token>\n+ <xml name="anndata_output_format">\n+ <param name="anndata_output_format" type="select" label="Format to write the annotated data matrix">\n+ <option value="loom">loom</option>\n+ <option value="h5ad">h5ad-formatted hdf5 (anndata)</option>\n+ </param>\n+ </xml>\n+ <xml name="anndata_modify_output_input">\n+ <conditional name="modify_anndata">\n+ <param name="modify_anndata" type="select" label="Return modify annotate data matrix?">\n+ <option value="true">Yes</option>\n+ <option value="false">No</option>\n+ </param>\n+ <when value="true">\n+ <expand macro="anndata_output_format"/>\n+ </when>\n+ <when value="false"/>\n+ </conditional>\n+ </xml>\n+ <xml name="anndata_outputs">\n+ <data name="anndata_out_h5ad" format="h5" from_work_dir="anndata.h5ad" label="${tool.name} on ${on_string}: Annotated data matrix">\n+ <filter>anndata_output_format == \'h5ad\'</filter>\n+ </data>\n+ <data name="anndata_out_loom" format="loom" from_work_dir="anndata.loom" label="${tool.name} on ${on_string}: Annotated data matrix">\n+ <filter>anndata_output_format == \'loom\'</filter>\n+ </data>\n+ </xml>\n+ <xml name="anndata_modify_outputs">\n+ <data name="anndata_out_h5ad" format="h5" from_work_dir="anndata.h5ad" label="${tool.name} on ${on_string}: Annotated'..b'ical sorting."/>\n+ <param argument="transitions" type="text" value="" label="Key corresponding to the matrix storing the arrows" help="Key for `.uns[\'paga\']`, e.g. \'transistions_confidence\'"/>\n+ <param argument="solid_edges" type="text" value="paga_connectivities" label="Key corresponding to the matrix storing the edges to be drawn solid black" help="Key for `.uns[\'paga\']`"/>\n+ <param argument="dashed_edges" type="text" value="" optional="true" label="Key corresponding to the matrix storing the edges to be drawn dashed grey" help="Key for `.uns[\'paga\']`. If not set, no dashed edges are drawn."/>\n+ <param argument="single_component" type="boolean" truevalue="True" falsevalue="False" checked="false" label="Restrict to largest connected component?" help=""/>\n+ <param argument="fontsize" type="integer" min="0" value="1" label="Font size for node labels" help=""/>\n+ <param argument="node_size_scale" type="float" min="0" value="1.0" label="Size of the nodes" help=""/>\n+ <param argument="node_size_power" type="float" min="0" value="0.5" label="Power with which groups sizes influence the radius of the nodes" help=""/>\n+ <param argument="edge_width_scale" type="float" min="0" value="5" label="Scale for edge width" help=""/>\n+ <param argument="min_edge_width" type="float" min="0" value="" optional="true" label="Min width of solid edges" help=""/>\n+ <param argument="max_edge_width" type="float" min="0" value="" optional="true" label="Max width of solid and dashed edges" help=""/>\n+ <param argument="arrowsize" type="integer" min="0" value="30" label="Arrow size" help="For directed graphs, choose the size of the arrow head head\'s length and width."/>\n+ <param argument="normalize_to_color" type="boolean" truevalue="True" falsevalue="False" checked="false" label="Normalize categorical plots to color or the underlying grouping?" help=""/>\n+ <expand macro="param_cmap"/>\n+ <expand macro="param_title"/>\n+ <expand macro="param_frameon"/>\n+ </xml>\n+ <token name="@CMD_params_pl_paga@"><![CDATA[\n+ threshold=$method.threshold,\n+#if str($method.groups) != \'\'\n+ #set $groups=([x.strip() for x in str($method.groups).split(\',\')])\n+ groups=$groups,\n+#else\n+ groups=None,\n+#end if\n+ color=\'$method.color\',\n+#if $method.pos\n+ pos=np.fromfile($method.pos, dtype=dt),\n+#end if\n+#if str($method.labels) != \'\'\n+ #set $labels=([x.strip() for x in str($method.labels).split(\',\')])\n+ labels=$labels,\n+#end if\n+ layout=\'$method.layout\',\n+#if $method.init_pos\n+ init_pos=np.fromfile($method.init_pos, dtype=dt),\n+#end if\n+ random_state=$method.random_state,\n+#if str($method.root) != \'\'\n+ #set $root=([int(x.strip()) for x in str($method.root).split(\',\')])\n+ root=$root,\n+#end if\n+#if $method.transitions\n+ transitions=\'$method.transitions\',\n+#end if\n+ solid_edges=\'$method.solid_edges\',\n+#if $method.dashed_edges\n+ dashed_edges=\'$method.dashed_edges\',\n+#end if\n+ single_component=$method.single_component,\n+ fontsize=$method.fontsize,\n+ node_size_scale=$method.node_size_scale,\n+ node_size_power=$method.node_size_power,\n+ edge_width_scale=$method.edge_width_scale,\n+#if $method.min_edge_width\n+ min_edge_width=$method.min_edge_width,\n+#end if\n+#if $method.max_edge_width\n+ max_edge_width=$method.max_edge_width,\n+#end if\n+ arrowsize=$method.arrowsize,\n+ normalize_to_color=$method.normalize_to_color,\n+ cmap=\'$method.cmap\',\n+#if $method.title\n+ title=\'$method.title\',\n+#end if\n+ frameon=$method.frameon,\n+ ]]>\n+ </token>\n+ <xml name="param_swap_axes">\n+ <param argument="swap_axes" type="boolean" truevalue="True" falsevalue="False" checked="false" label="Swap axes?" help="By default, the x axis contains `var_names` (e.g. genes) and the y axis the `groupby` categories (if any). By setting `swap_axes` then x are the `groupby` categories and y the `var_names`."/>\n+ </xml>\n+</macros>\n' |
| b |
| diff -r 000000000000 -r 6ea5a05a260a test-data/krumsiek11.h5ad |
| b |
| Binary file test-data/krumsiek11.h5ad has changed |
| b |
| diff -r 000000000000 -r 6ea5a05a260a test-data/krumsiek11.loom |
| b |
| Binary file test-data/krumsiek11.loom has changed |
| b |
| diff -r 000000000000 -r 6ea5a05a260a test-data/krumsiek11_counts_per_cell --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/krumsiek11_counts_per_cell Mon Mar 04 10:15:02 2019 -0500 |
| b |
| b'@@ -0,0 +1,640 @@\n+2.408400297164916992e+00\n+2.452799797058105469e+00\n+2.441299915313720703e+00\n+2.371799945831298828e+00\n+2.295799970626831055e+00\n+2.236100196838378906e+00\n+2.159400224685668945e+00\n+2.094000101089477539e+00\n+2.050699949264526367e+00\n+2.009300231933593750e+00\n+1.965499877929687500e+00\n+1.940399885177612305e+00\n+1.925999999046325684e+00\n+1.915199875831604004e+00\n+1.916800022125244141e+00\n+1.921400070190429688e+00\n+1.931500196456909180e+00\n+1.958499908447265625e+00\n+1.997500061988830566e+00\n+2.039499998092651367e+00\n+2.084599733352661133e+00\n+2.127799987792968750e+00\n+2.187099933624267578e+00\n+2.239099979400634766e+00\n+2.285900115966796875e+00\n+2.337300062179565430e+00\n+2.391999959945678711e+00\n+2.438399791717529297e+00\n+2.489500045776367188e+00\n+2.545399904251098633e+00\n+2.599499940872192383e+00\n+2.647500276565551758e+00\n+2.696399927139282227e+00\n+2.719100236892700195e+00\n+2.758599758148193359e+00\n+2.798499822616577148e+00\n+2.817299842834472656e+00\n+2.856800079345703125e+00\n+2.882500171661376953e+00\n+2.892000198364257812e+00\n+2.910799741744995117e+00\n+2.925500154495239258e+00\n+2.948799848556518555e+00\n+2.968800067901611328e+00\n+2.992099761962890625e+00\n+3.009699821472167969e+00\n+3.028200149536132812e+00\n+3.031499862670898438e+00\n+3.045699834823608398e+00\n+3.049900054931640625e+00\n+3.059900045394897461e+00\n+3.072500228881835938e+00\n+3.077599763870239258e+00\n+3.089499950408935547e+00\n+3.088899850845336914e+00\n+3.107500076293945312e+00\n+3.107999801635742188e+00\n+3.108199834823608398e+00\n+3.120700120925903320e+00\n+3.125699996948242188e+00\n+3.139300107955932617e+00\n+3.160399913787841797e+00\n+3.179100036621093750e+00\n+3.196399927139282227e+00\n+3.225399732589721680e+00\n+3.246099948883056641e+00\n+3.276799917221069336e+00\n+3.294199943542480469e+00\n+3.331000328063964844e+00\n+3.366000175476074219e+00\n+3.403100013732910156e+00\n+3.429600000381469727e+00\n+3.460299730300903320e+00\n+3.506799936294555664e+00\n+3.535099744796752930e+00\n+3.563699722290039062e+00\n+3.601699829101562500e+00\n+3.628099918365478516e+00\n+3.656300067901611328e+00\n+3.690200090408325195e+00\n+3.716900110244750977e+00\n+3.735100030899047852e+00\n+3.751500129699707031e+00\n+3.772299766540527344e+00\n+3.786999940872192383e+00\n+3.799900054931640625e+00\n+3.813199996948242188e+00\n+3.829000234603881836e+00\n+3.841199874877929688e+00\n+3.855699777603149414e+00\n+3.879299879074096680e+00\n+3.888599872589111328e+00\n+3.891200065612792969e+00\n+3.899099826812744141e+00\n+3.896700143814086914e+00\n+3.900700330734252930e+00\n+3.902399778366088867e+00\n+3.909000158309936523e+00\n+3.924799919128417969e+00\n+3.909100055694580078e+00\n+3.908500194549560547e+00\n+3.913800001144409180e+00\n+3.918300151824951172e+00\n+3.918600082397460938e+00\n+3.923599958419799805e+00\n+3.930300235748291016e+00\n+3.933600187301635742e+00\n+3.939800024032592773e+00\n+3.939800024032592773e+00\n+3.940799951553344727e+00\n+3.939599990844726562e+00\n+3.949400186538696289e+00\n+3.946899890899658203e+00\n+3.949199914932250977e+00\n+3.959100008010864258e+00\n+3.953099966049194336e+00\n+3.948199987411499023e+00\n+3.958700180053710938e+00\n+3.947399854660034180e+00\n+3.947599887847900391e+00\n+3.953999996185302734e+00\n+3.963799953460693359e+00\n+3.958499908447265625e+00\n+3.948000192642211914e+00\n+3.955900192260742188e+00\n+3.960099935531616211e+00\n+3.953900098800659180e+00\n+3.940199851989746094e+00\n+3.943799972534179688e+00\n+3.938899993896484375e+00\n+3.939199686050415039e+00\n+3.939899921417236328e+00\n+3.942100048065185547e+00\n+3.947299718856811523e+00\n+3.950499773025512695e+00\n+3.946299791336059570e+00\n+3.943099975585937500e+00\n+3.937799930572509766e+00\n+3.936500072479248047e+00\n+3.951900005340576172e+00\n+3.955199956893920898e+00\n+3.950200080871582031e+00\n+3.952800035476684570e+00\n+3.943200111389160156e+00\n+3.935600042343139648e+00\n+3.929900169372558594e+00\n+3.941400051116943359e+00\n+3.930999994277954102e+00\n+3.941400051116943359e+00\n+3.955500125885009766e+00\n+3.956299781799316406e+00\n+3.946699857711791992e+00\n+3.932600021362304688e+00\n+3.'..b'3299989700317383e+00\n+2.159399986267089844e+00\n+2.099900007247924805e+00\n+2.056699991226196289e+00\n+2.025199890136718750e+00\n+1.996799945831298828e+00\n+1.957400202751159668e+00\n+1.931800007820129395e+00\n+1.910700082778930664e+00\n+1.889699935913085938e+00\n+1.894500017166137695e+00\n+1.883400201797485352e+00\n+1.879799962043762207e+00\n+1.875000000000000000e+00\n+1.869399905204772949e+00\n+1.858600139617919922e+00\n+1.871700048446655273e+00\n+1.882499933242797852e+00\n+1.887800097465515137e+00\n+1.892300009727478027e+00\n+1.885900020599365234e+00\n+1.903299808502197266e+00\n+1.912000060081481934e+00\n+1.921299934387207031e+00\n+1.914299964904785156e+00\n+1.915700197219848633e+00\n+1.928300023078918457e+00\n+1.931900024414062500e+00\n+1.930599927902221680e+00\n+1.941800117492675781e+00\n+1.945299983024597168e+00\n+1.956899881362915039e+00\n+1.964700222015380859e+00\n+1.967999935150146484e+00\n+1.966400027275085449e+00\n+1.972699880599975586e+00\n+1.986699938774108887e+00\n+1.998100042343139648e+00\n+2.006099939346313477e+00\n+2.014899969100952148e+00\n+2.035799980163574219e+00\n+2.059900045394897461e+00\n+2.089900016784667969e+00\n+2.121299982070922852e+00\n+2.151399850845336914e+00\n+2.189300060272216797e+00\n+2.239999771118164062e+00\n+2.283900260925292969e+00\n+2.331199884414672852e+00\n+2.380800008773803711e+00\n+2.435999870300292969e+00\n+2.480200052261352539e+00\n+2.528899908065795898e+00\n+2.568600177764892578e+00\n+2.605000019073486328e+00\n+2.632200241088867188e+00\n+2.671899795532226562e+00\n+2.700799942016601562e+00\n+2.706700086593627930e+00\n+2.725800037384033203e+00\n+2.728600025177001953e+00\n+2.746000051498413086e+00\n+2.749099969863891602e+00\n+2.746299982070922852e+00\n+2.745100021362304688e+00\n+2.740399837493896484e+00\n+2.721600055694580078e+00\n+2.733300209045410156e+00\n+2.745200157165527344e+00\n+2.753600120544433594e+00\n+2.758900165557861328e+00\n+2.772200107574462891e+00\n+2.782299995422363281e+00\n+2.797100067138671875e+00\n+2.812000274658203125e+00\n+2.839200019836425781e+00\n+2.853300094604492188e+00\n+2.865500211715698242e+00\n+2.880899906158447266e+00\n+2.884700059890747070e+00\n+2.877900123596191406e+00\n+2.896800041198730469e+00\n+2.896899938583374023e+00\n+2.901299953460693359e+00\n+2.904000043869018555e+00\n+2.914000034332275391e+00\n+2.928899765014648438e+00\n+2.939800024032592773e+00\n+2.936100006103515625e+00\n+2.950000047683715820e+00\n+2.941200017929077148e+00\n+2.934599876403808594e+00\n+2.946899890899658203e+00\n+2.952399969100952148e+00\n+2.942699909210205078e+00\n+2.946599960327148438e+00\n+2.946300029754638672e+00\n+2.943899869918823242e+00\n+2.942800045013427734e+00\n+2.943900108337402344e+00\n+2.951200008392333984e+00\n+2.949299812316894531e+00\n+2.955400228500366211e+00\n+2.943600177764892578e+00\n+2.935999870300292969e+00\n+2.948500156402587891e+00\n+2.950099945068359375e+00\n+2.951200008392333984e+00\n+2.960999965667724609e+00\n+2.963699817657470703e+00\n+2.971600294113159180e+00\n+2.975999832153320312e+00\n+2.958300113677978516e+00\n+2.944900035858154297e+00\n+2.919999837875366211e+00\n+2.921499967575073242e+00\n+2.922800064086914062e+00\n+2.929299831390380859e+00\n+2.933599948883056641e+00\n+2.934400081634521484e+00\n+2.943200111389160156e+00\n+2.958299875259399414e+00\n+2.960800170898437500e+00\n+2.952000141143798828e+00\n+2.953899860382080078e+00\n+2.946300029754638672e+00\n+2.940300226211547852e+00\n+2.945899724960327148e+00\n+2.938000202178955078e+00\n+2.931699991226196289e+00\n+2.925199985504150391e+00\n+2.920900106430053711e+00\n+2.926300048828125000e+00\n+2.927299976348876953e+00\n+2.919699907302856445e+00\n+2.934800148010253906e+00\n+2.934599876403808594e+00\n+2.930900096893310547e+00\n+2.936100006103515625e+00\n+2.930900096893310547e+00\n+2.926499843597412109e+00\n+2.933099985122680664e+00\n+2.932799816131591797e+00\n+2.937399864196777344e+00\n+2.932799816131591797e+00\n+2.935299873352050781e+00\n+2.923399925231933594e+00\n+2.914299964904785156e+00\n+2.917200088500976562e+00\n+2.901000022888183594e+00\n+2.908900022506713867e+00\n+2.912899732589721680e+00\n+2.921400070190429688e+00\n+2.925299882888793945e+00\n' |
| b |
| diff -r 000000000000 -r 6ea5a05a260a test-data/paul15_subsample.h5ad |
| b |
| Binary file test-data/paul15_subsample.h5ad has changed |
| b |
| diff -r 000000000000 -r 6ea5a05a260a test-data/pbmc68k_reduced.h5ad |
| b |
| Binary file test-data/pbmc68k_reduced.h5ad has changed |
| b |
| diff -r 000000000000 -r 6ea5a05a260a test-data/pl.clustermap.krumsiek11.png |
| b |
| Binary file test-data/pl.clustermap.krumsiek11.png has changed |
| b |
| diff -r 000000000000 -r 6ea5a05a260a test-data/pl.diffmap.neighbors_gauss_braycurtis.recipe_weinreb17.paul15_subsampl.png |
| b |
| Binary file test-data/pl.diffmap.neighbors_gauss_braycurtis.recipe_weinreb17.paul15_subsampl.png has changed |
| b |
| diff -r 000000000000 -r 6ea5a05a260a test-data/pl.diffmap.neighbors_gauss_braycurtis.recipe_weinreb17.paul15_subsample.png |
| b |
| Binary file test-data/pl.diffmap.neighbors_gauss_braycurtis.recipe_weinreb17.paul15_subsample.png has changed |
| b |
| diff -r 000000000000 -r 6ea5a05a260a test-data/pl.dotplot.krumsiek11.png |
| b |
| Binary file test-data/pl.dotplot.krumsiek11.png has changed |
| b |
| diff -r 000000000000 -r 6ea5a05a260a test-data/pl.dpt_timeseries.dpt.diffmap.neighbors_gauss_braycurtis.recipe_weinreb17.paul15_subsample.png |
| b |
| Binary file test-data/pl.dpt_timeseries.dpt.diffmap.neighbors_gauss_braycurtis.recipe_weinreb17.paul15_subsample.png has changed |
| b |
| diff -r 000000000000 -r 6ea5a05a260a test-data/pl.heatmap.krumsiek11.png |
| b |
| Binary file test-data/pl.heatmap.krumsiek11.png has changed |
| b |
| diff -r 000000000000 -r 6ea5a05a260a test-data/pl.highest_expr_genes.filter_genes_dispersion.krumsiek11-seurat.png |
| b |
| Binary file test-data/pl.highest_expr_genes.filter_genes_dispersion.krumsiek11-seurat.png has changed |
| b |
| diff -r 000000000000 -r 6ea5a05a260a test-data/pl.matrixplot.krumsiek11.png |
| b |
| Binary file test-data/pl.matrixplot.krumsiek11.png has changed |
| b |
| diff -r 000000000000 -r 6ea5a05a260a test-data/pl.paga.paul15_gauss_braycurtis.png |
| b |
| Binary file test-data/pl.paga.paul15_gauss_braycurtis.png has changed |
| b |
| diff -r 000000000000 -r 6ea5a05a260a test-data/pl.pca.pbmc68k_reduced.CD3D_CD79A_components_2d.pdf |
| b |
| Binary file test-data/pl.pca.pbmc68k_reduced.CD3D_CD79A_components_2d.pdf has changed |
| b |
| diff -r 000000000000 -r 6ea5a05a260a test-data/pl.pca_loadings.pp.pca.krumsiek11.png |
| b |
| Binary file test-data/pl.pca_loadings.pp.pca.krumsiek11.png has changed |
| b |
| diff -r 000000000000 -r 6ea5a05a260a test-data/pl.pca_overview.pp.pca.krumsiek11.png |
| b |
| Binary file test-data/pl.pca_overview.pp.pca.krumsiek11.png has changed |
| b |
| diff -r 000000000000 -r 6ea5a05a260a test-data/pl.pca_variance_ratio.pp.pca.krumsiek11.png |
| b |
| Binary file test-data/pl.pca_variance_ratio.pp.pca.krumsiek11.png has changed |
| b |
| diff -r 000000000000 -r 6ea5a05a260a test-data/pl.scatter.krumsiek11.png |
| b |
| Binary file test-data/pl.scatter.krumsiek11.png has changed |
| b |
| diff -r 000000000000 -r 6ea5a05a260a test-data/pl.scatter.pca.krumsiek11.png |
| b |
| Binary file test-data/pl.scatter.pca.krumsiek11.png has changed |
| b |
| diff -r 000000000000 -r 6ea5a05a260a test-data/pl.tsne.krumsiek11.png |
| b |
| Binary file test-data/pl.tsne.krumsiek11.png has changed |
| b |
| diff -r 000000000000 -r 6ea5a05a260a test-data/pl.umap.neighbors_umap_euclidean.recipe_weinreb17.paul15_subsample.png |
| b |
| Binary file test-data/pl.umap.neighbors_umap_euclidean.recipe_weinreb17.paul15_subsample.png has changed |
| b |
| diff -r 000000000000 -r 6ea5a05a260a test-data/pl.violin.pbmc68k_reduced_custom.png |
| b |
| Binary file test-data/pl.violin.pbmc68k_reduced_custom.png has changed |
| b |
| diff -r 000000000000 -r 6ea5a05a260a test-data/pp.filter_cells.krumsiek11-min_counts.h5ad |
| b |
| Binary file test-data/pp.filter_cells.krumsiek11-min_counts.h5ad has changed |
| b |
| diff -r 000000000000 -r 6ea5a05a260a test-data/pp.filter_cells.krumsiek11-min_counts.loom |
| b |
| Binary file test-data/pp.filter_cells.krumsiek11-min_counts.loom has changed |
| b |
| diff -r 000000000000 -r 6ea5a05a260a test-data/pp.filter_cells.number_per_cell.krumsiek11-max_genes.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/pp.filter_cells.number_per_cell.krumsiek11-max_genes.tabular Mon Mar 04 10:15:02 2019 -0500 |
| b |
| b'@@ -0,0 +1,641 @@\n+\tcell_subset\tnumber_per_cell\n+0\tTrue\t9\n+1\tTrue\t9\n+2\tTrue\t9\n+3\tTrue\t8\n+4\tTrue\t8\n+5\tTrue\t8\n+6\tTrue\t8\n+7\tTrue\t7\n+8\tTrue\t8\n+9\tTrue\t8\n+10\tTrue\t7\n+11\tTrue\t7\n+12\tTrue\t7\n+13\tTrue\t7\n+14\tTrue\t8\n+15\tTrue\t10\n+16\tTrue\t10\n+17\tTrue\t10\n+18\tTrue\t11\n+19\tTrue\t11\n+20\tTrue\t11\n+21\tTrue\t11\n+22\tTrue\t11\n+23\tTrue\t11\n+24\tTrue\t11\n+25\tTrue\t11\n+26\tTrue\t11\n+27\tTrue\t11\n+28\tTrue\t11\n+29\tTrue\t11\n+30\tTrue\t11\n+31\tTrue\t11\n+32\tTrue\t11\n+33\tTrue\t11\n+34\tTrue\t11\n+35\tTrue\t11\n+36\tTrue\t11\n+37\tTrue\t11\n+38\tTrue\t11\n+39\tTrue\t11\n+40\tTrue\t11\n+41\tTrue\t11\n+42\tTrue\t11\n+43\tTrue\t11\n+44\tTrue\t11\n+45\tTrue\t11\n+46\tTrue\t11\n+47\tTrue\t11\n+48\tTrue\t10\n+49\tTrue\t10\n+50\tTrue\t10\n+51\tTrue\t10\n+52\tTrue\t10\n+53\tTrue\t10\n+54\tTrue\t10\n+55\tTrue\t10\n+56\tTrue\t11\n+57\tTrue\t11\n+58\tTrue\t11\n+59\tTrue\t10\n+60\tTrue\t10\n+61\tTrue\t11\n+62\tTrue\t10\n+63\tTrue\t11\n+64\tTrue\t10\n+65\tTrue\t10\n+66\tTrue\t11\n+67\tTrue\t11\n+68\tTrue\t11\n+69\tTrue\t10\n+70\tTrue\t10\n+71\tTrue\t10\n+72\tTrue\t10\n+73\tTrue\t10\n+74\tTrue\t11\n+75\tTrue\t10\n+76\tTrue\t10\n+77\tTrue\t10\n+78\tTrue\t9\n+79\tTrue\t10\n+80\tTrue\t9\n+81\tTrue\t9\n+82\tTrue\t10\n+83\tTrue\t9\n+84\tTrue\t9\n+85\tTrue\t9\n+86\tTrue\t9\n+87\tTrue\t9\n+88\tTrue\t9\n+89\tTrue\t9\n+90\tTrue\t9\n+91\tTrue\t10\n+92\tTrue\t10\n+93\tTrue\t9\n+94\tTrue\t9\n+95\tTrue\t9\n+96\tTrue\t9\n+97\tTrue\t7\n+98\tTrue\t7\n+99\tTrue\t6\n+100\tTrue\t6\n+101\tTrue\t7\n+102\tTrue\t8\n+103\tTrue\t8\n+104\tTrue\t8\n+105\tTrue\t8\n+106\tTrue\t9\n+107\tTrue\t9\n+108\tTrue\t9\n+109\tTrue\t8\n+110\tTrue\t8\n+111\tTrue\t10\n+112\tTrue\t9\n+113\tTrue\t8\n+114\tTrue\t9\n+115\tTrue\t10\n+116\tTrue\t9\n+117\tTrue\t8\n+118\tTrue\t7\n+119\tTrue\t7\n+120\tTrue\t7\n+121\tTrue\t7\n+122\tTrue\t9\n+123\tTrue\t9\n+124\tTrue\t9\n+125\tTrue\t8\n+126\tTrue\t7\n+127\tTrue\t6\n+128\tTrue\t6\n+129\tTrue\t8\n+130\tTrue\t8\n+131\tTrue\t8\n+132\tTrue\t8\n+133\tTrue\t10\n+134\tTrue\t10\n+135\tTrue\t8\n+136\tTrue\t6\n+137\tTrue\t6\n+138\tTrue\t8\n+139\tTrue\t9\n+140\tTrue\t8\n+141\tTrue\t7\n+142\tTrue\t7\n+143\tTrue\t8\n+144\tTrue\t7\n+145\tTrue\t7\n+146\tTrue\t7\n+147\tTrue\t5\n+148\tTrue\t6\n+149\tTrue\t8\n+150\tTrue\t9\n+151\tTrue\t6\n+152\tTrue\t6\n+153\tTrue\t6\n+154\tTrue\t7\n+155\tTrue\t8\n+156\tTrue\t7\n+157\tTrue\t7\n+158\tTrue\t7\n+159\tTrue\t8\n+160\tTrue\t9\n+161\tTrue\t8\n+162\tTrue\t8\n+163\tTrue\t9\n+164\tTrue\t9\n+165\tTrue\t9\n+166\tTrue\t8\n+167\tTrue\t8\n+168\tTrue\t9\n+169\tTrue\t9\n+170\tTrue\t8\n+171\tTrue\t9\n+172\tTrue\t9\n+173\tTrue\t10\n+174\tTrue\t10\n+175\tTrue\t10\n+176\tTrue\t10\n+177\tTrue\t10\n+178\tTrue\t10\n+179\tTrue\t10\n+180\tTrue\t10\n+181\tTrue\t10\n+182\tTrue\t10\n+183\tTrue\t10\n+184\tTrue\t10\n+185\tTrue\t10\n+186\tTrue\t10\n+187\tTrue\t10\n+188\tTrue\t11\n+189\tTrue\t11\n+190\tTrue\t11\n+191\tTrue\t11\n+192\tTrue\t11\n+193\tTrue\t11\n+194\tTrue\t11\n+195\tTrue\t11\n+196\tTrue\t11\n+197\tTrue\t11\n+198\tTrue\t11\n+199\tTrue\t11\n+200\tTrue\t11\n+201\tTrue\t11\n+202\tTrue\t11\n+203\tTrue\t11\n+204\tTrue\t11\n+205\tTrue\t11\n+206\tTrue\t11\n+207\tTrue\t11\n+208\tTrue\t11\n+209\tTrue\t11\n+210\tTrue\t11\n+211\tTrue\t11\n+212\tTrue\t11\n+213\tTrue\t11\n+214\tTrue\t11\n+215\tTrue\t11\n+216\tTrue\t11\n+217\tTrue\t11\n+218\tTrue\t11\n+219\tTrue\t11\n+220\tTrue\t11\n+221\tTrue\t11\n+222\tTrue\t11\n+223\tTrue\t11\n+224\tTrue\t11\n+225\tTrue\t11\n+226\tTrue\t11\n+227\tTrue\t11\n+228\tTrue\t11\n+229\tTrue\t11\n+230\tTrue\t11\n+231\tTrue\t11\n+232\tTrue\t11\n+233\tTrue\t11\n+234\tTrue\t11\n+235\tTrue\t11\n+236\tTrue\t11\n+237\tTrue\t11\n+238\tTrue\t11\n+239\tTrue\t11\n+240\tTrue\t11\n+241\tTrue\t11\n+242\tTrue\t11\n+243\tTrue\t11\n+244\tTrue\t11\n+245\tTrue\t11\n+246\tTrue\t11\n+247\tTrue\t11\n+248\tTrue\t11\n+249\tTrue\t11\n+250\tTrue\t11\n+251\tTrue\t11\n+252\tTrue\t11\n+253\tTrue\t11\n+254\tTrue\t11\n+255\tTrue\t11\n+256\tTrue\t11\n+257\tTrue\t11\n+258\tTrue\t11\n+259\tTrue\t11\n+260\tTrue\t11\n+261\tTrue\t11\n+262\tTrue\t11\n+263\tTrue\t11\n+264\tTrue\t11\n+265\tTrue\t11\n+266\tTrue\t11\n+267\tTrue\t11\n+268\tTrue\t11\n+269\tTrue\t11\n+270\tTrue\t11\n+271\tTrue\t11\n+272\tTrue\t10\n+273\tTrue\t11\n+274\tTrue\t11\n+275\tTrue\t11\n+276\tTrue\t11\n+277\tTrue\t11\n+278\tTrue\t11\n+279\tTrue\t10\n+280\tTrue\t11\n+281\tTrue\t9\n+282\tTrue\t9\n+283\tTrue\t8\n+284\tTrue\t9\n+285\tTrue\t9\n+286\tTrue\t10\n+287\tTrue\t9\n+288\tTrue\t9\n+289\tTrue\t9\n+290\tTrue\t9\n+291\tTrue\t9\n+292\tTrue\t9\n+293\tTrue\t10\n+294\tTrue\t10\n+295\tTrue\t10\n+296\tTrue\t10\n+297\tTrue\t9\n+298\tTrue\t10\n+299\tTrue\t9\n+300\tTrue\t8\n+301\tTrue\t8\n+302\tTrue\t8\n+303\tTrue\t8\n+304\tTrue\t8\n+305\tTrue\t9\n+306\tTrue\t8\n+307\tTrue\t8\n+308\tTrue\t8\n+309\tTrue\t8\n+310\tTrue\t9\n+311\tTrue\t8\n+312\tTrue\t9\n+313\tTrue\t9\n+314\tTrue\t10\n+315\tTrue\t10\n+316\tTrue\t10\n+317\tTrue\t10\n+318\tTrue\t10\n+319\tTrue\t10\n+320\tTrue\t4\n+321\tTrue\t8\n+322\tT'..b'\t8\n+324\tTrue\t8\n+325\tTrue\t7\n+326\tTrue\t8\n+327\tTrue\t8\n+328\tTrue\t7\n+329\tTrue\t9\n+330\tTrue\t8\n+331\tTrue\t9\n+332\tTrue\t8\n+333\tTrue\t8\n+334\tTrue\t8\n+335\tTrue\t10\n+336\tTrue\t10\n+337\tTrue\t9\n+338\tTrue\t10\n+339\tTrue\t10\n+340\tTrue\t10\n+341\tTrue\t10\n+342\tTrue\t10\n+343\tTrue\t10\n+344\tTrue\t10\n+345\tTrue\t11\n+346\tTrue\t11\n+347\tTrue\t11\n+348\tTrue\t11\n+349\tTrue\t11\n+350\tTrue\t11\n+351\tTrue\t11\n+352\tTrue\t11\n+353\tTrue\t11\n+354\tTrue\t11\n+355\tTrue\t11\n+356\tTrue\t11\n+357\tTrue\t11\n+358\tTrue\t11\n+359\tTrue\t11\n+360\tTrue\t11\n+361\tTrue\t11\n+362\tTrue\t11\n+363\tTrue\t11\n+364\tTrue\t11\n+365\tTrue\t11\n+366\tTrue\t11\n+367\tTrue\t11\n+368\tTrue\t11\n+369\tTrue\t11\n+370\tTrue\t11\n+371\tTrue\t11\n+372\tTrue\t11\n+373\tTrue\t11\n+374\tTrue\t11\n+375\tTrue\t11\n+376\tTrue\t11\n+377\tTrue\t11\n+378\tTrue\t11\n+379\tTrue\t11\n+380\tTrue\t11\n+381\tTrue\t11\n+382\tTrue\t11\n+383\tTrue\t11\n+384\tTrue\t11\n+385\tTrue\t11\n+386\tTrue\t11\n+387\tTrue\t11\n+388\tTrue\t11\n+389\tTrue\t11\n+390\tTrue\t11\n+391\tTrue\t11\n+392\tTrue\t11\n+393\tTrue\t11\n+394\tTrue\t11\n+395\tTrue\t11\n+396\tTrue\t11\n+397\tTrue\t11\n+398\tTrue\t11\n+399\tTrue\t11\n+400\tTrue\t11\n+401\tTrue\t11\n+402\tTrue\t11\n+403\tTrue\t11\n+404\tTrue\t11\n+405\tTrue\t11\n+406\tTrue\t11\n+407\tTrue\t11\n+408\tTrue\t11\n+409\tTrue\t11\n+410\tTrue\t11\n+411\tTrue\t11\n+412\tTrue\t11\n+413\tTrue\t11\n+414\tTrue\t11\n+415\tTrue\t11\n+416\tTrue\t11\n+417\tTrue\t11\n+418\tTrue\t11\n+419\tTrue\t11\n+420\tTrue\t11\n+421\tTrue\t11\n+422\tTrue\t11\n+423\tTrue\t11\n+424\tTrue\t11\n+425\tTrue\t11\n+426\tTrue\t11\n+427\tTrue\t11\n+428\tTrue\t11\n+429\tTrue\t11\n+430\tTrue\t11\n+431\tTrue\t11\n+432\tTrue\t11\n+433\tTrue\t11\n+434\tTrue\t11\n+435\tTrue\t11\n+436\tTrue\t11\n+437\tTrue\t11\n+438\tTrue\t11\n+439\tTrue\t11\n+440\tTrue\t11\n+441\tTrue\t11\n+442\tTrue\t11\n+443\tTrue\t11\n+444\tTrue\t11\n+445\tTrue\t11\n+446\tTrue\t10\n+447\tTrue\t10\n+448\tTrue\t10\n+449\tTrue\t10\n+450\tTrue\t10\n+451\tTrue\t11\n+452\tTrue\t11\n+453\tTrue\t11\n+454\tTrue\t10\n+455\tTrue\t10\n+456\tTrue\t11\n+457\tTrue\t10\n+458\tTrue\t10\n+459\tTrue\t11\n+460\tTrue\t11\n+461\tTrue\t10\n+462\tTrue\t9\n+463\tTrue\t10\n+464\tTrue\t10\n+465\tTrue\t10\n+466\tTrue\t10\n+467\tTrue\t9\n+468\tTrue\t10\n+469\tTrue\t10\n+470\tTrue\t11\n+471\tTrue\t11\n+472\tTrue\t9\n+473\tTrue\t9\n+474\tTrue\t9\n+475\tTrue\t9\n+476\tTrue\t9\n+477\tTrue\t10\n+478\tTrue\t10\n+479\tTrue\t9\n+480\tTrue\t8\n+481\tTrue\t10\n+482\tTrue\t10\n+483\tTrue\t10\n+484\tTrue\t8\n+485\tTrue\t8\n+486\tTrue\t9\n+487\tTrue\t8\n+488\tTrue\t9\n+489\tTrue\t10\n+490\tTrue\t11\n+491\tTrue\t11\n+492\tTrue\t11\n+493\tTrue\t9\n+494\tTrue\t10\n+495\tTrue\t10\n+496\tTrue\t10\n+497\tTrue\t10\n+498\tTrue\t11\n+499\tTrue\t11\n+500\tTrue\t11\n+501\tTrue\t11\n+502\tTrue\t11\n+503\tTrue\t11\n+504\tTrue\t11\n+505\tTrue\t11\n+506\tTrue\t11\n+507\tTrue\t11\n+508\tTrue\t11\n+509\tTrue\t11\n+510\tTrue\t11\n+511\tTrue\t11\n+512\tTrue\t11\n+513\tTrue\t11\n+514\tTrue\t11\n+515\tTrue\t11\n+516\tTrue\t11\n+517\tTrue\t11\n+518\tTrue\t11\n+519\tTrue\t11\n+520\tTrue\t11\n+521\tTrue\t11\n+522\tTrue\t11\n+523\tTrue\t11\n+524\tTrue\t11\n+525\tTrue\t11\n+526\tTrue\t11\n+527\tTrue\t11\n+528\tTrue\t11\n+529\tTrue\t11\n+530\tTrue\t11\n+531\tTrue\t11\n+532\tTrue\t11\n+533\tTrue\t11\n+534\tTrue\t11\n+535\tTrue\t11\n+536\tTrue\t10\n+537\tTrue\t10\n+538\tTrue\t10\n+539\tTrue\t10\n+540\tTrue\t10\n+541\tTrue\t10\n+542\tTrue\t11\n+543\tTrue\t11\n+544\tTrue\t11\n+545\tTrue\t11\n+546\tTrue\t11\n+547\tTrue\t10\n+548\tTrue\t9\n+549\tTrue\t9\n+550\tTrue\t10\n+551\tTrue\t11\n+552\tTrue\t10\n+553\tTrue\t9\n+554\tTrue\t9\n+555\tTrue\t9\n+556\tTrue\t8\n+557\tTrue\t9\n+558\tTrue\t7\n+559\tTrue\t8\n+560\tTrue\t8\n+561\tTrue\t10\n+562\tTrue\t9\n+563\tTrue\t8\n+564\tTrue\t8\n+565\tTrue\t8\n+566\tTrue\t8\n+567\tTrue\t8\n+568\tTrue\t6\n+569\tTrue\t6\n+570\tTrue\t6\n+571\tTrue\t6\n+572\tTrue\t8\n+573\tTrue\t8\n+574\tTrue\t7\n+575\tTrue\t9\n+576\tTrue\t7\n+577\tTrue\t7\n+578\tTrue\t8\n+579\tTrue\t8\n+580\tTrue\t6\n+581\tTrue\t7\n+582\tTrue\t7\n+583\tTrue\t8\n+584\tTrue\t6\n+585\tTrue\t5\n+586\tTrue\t5\n+587\tTrue\t5\n+588\tTrue\t6\n+589\tTrue\t7\n+590\tTrue\t6\n+591\tTrue\t8\n+592\tTrue\t7\n+593\tTrue\t7\n+594\tTrue\t8\n+595\tTrue\t7\n+596\tTrue\t7\n+597\tTrue\t8\n+598\tTrue\t5\n+599\tTrue\t4\n+600\tTrue\t5\n+601\tTrue\t6\n+602\tTrue\t5\n+603\tTrue\t6\n+604\tTrue\t7\n+605\tTrue\t7\n+606\tTrue\t9\n+607\tTrue\t10\n+608\tTrue\t8\n+609\tTrue\t8\n+610\tTrue\t10\n+611\tTrue\t10\n+612\tTrue\t9\n+613\tTrue\t8\n+614\tTrue\t8\n+615\tTrue\t8\n+616\tTrue\t7\n+617\tTrue\t8\n+618\tTrue\t7\n+619\tTrue\t6\n+620\tTrue\t6\n+621\tTrue\t7\n+622\tTrue\t7\n+623\tTrue\t7\n+624\tTrue\t8\n+625\tTrue\t6\n+626\tTrue\t7\n+627\tTrue\t7\n+628\tTrue\t7\n+629\tTrue\t6\n+630\tTrue\t5\n+631\tTrue\t7\n+632\tTrue\t6\n+633\tTrue\t6\n+634\tTrue\t7\n+635\tTrue\t6\n+636\tTrue\t8\n+637\tTrue\t8\n+638\tTrue\t6\n+639\tTrue\t8\n' |
| b |
| diff -r 000000000000 -r 6ea5a05a260a test-data/pp.filter_genes.krumsiek11-min_counts.h5ad |
| b |
| Binary file test-data/pp.filter_genes.krumsiek11-min_counts.h5ad has changed |
| b |
| diff -r 000000000000 -r 6ea5a05a260a test-data/pp.filter_genes.number_per_gene.krumsiek11-min_counts.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/pp.filter_genes.number_per_gene.krumsiek11-min_counts.tabular Mon Mar 04 10:15:02 2019 -0500 |
| b |
| @@ -0,0 +1,12 @@ +index n_counts +Gata2 163.95355 +Gata1 203.95117 +Fog1 83.94181 +EKLF 70.69286 +Fli1 57.56072 +SCL 202.67444 +Cebpa 469.87094 +Pu.1 250.78569 +cJun 188.10158 +EgrNab 164.99693 +Gfi1 159.99155 |
| b |
| diff -r 000000000000 -r 6ea5a05a260a test-data/pp.filter_genes.number_per_gene.pbmc68k_reduced-max_cells.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/pp.filter_genes.number_per_gene.pbmc68k_reduced-max_cells.tabular Mon Mar 04 10:15:02 2019 -0500 |
| b |
| @@ -0,0 +1,222 @@ + gene_subset number_per_gene +0 True 34 +1 True 123 +2 True 281 +3 True 54 +4 True 253 +5 True 63 +6 True 9 +7 True 266 +8 True 101 +9 True 233 +10 True 267 +11 True 285 +12 True 332 +13 True 197 +14 True 158 +15 True 64 +16 True 285 +17 True 229 +18 True 43 +19 True 199 +20 True 271 +21 True 318 +22 True 132 +23 True 83 +24 True 88 +25 True 87 +26 True 71 +27 True 258 +28 True 58 +29 True 348 +30 True 280 +31 True 150 +32 True 121 +33 True 237 +34 True 29 +35 True 220 +36 True 103 +37 True 87 +38 True 115 +39 True 100 +40 True 139 +41 True 23 +42 True 162 +43 True 76 +44 True 180 +45 True 51 +46 True 244 +47 True 132 +48 True 244 +49 True 82 +50 True 172 +51 True 27 +52 True 100 +53 True 327 +54 True 277 +55 True 282 +56 True 245 +57 True 21 +58 True 52 +59 True 19 +60 True 227 +61 True 288 +62 True 274 +63 True 301 +64 True 316 +65 True 314 +66 True 271 +67 True 270 +68 True 283 +69 True 245 +70 True 263 +71 True 312 +72 True 285 +73 True 228 +74 True 170 +75 True 11 +76 True 228 +77 True 192 +78 True 140 +79 True 15 +80 True 22 +81 True 10 +82 True 233 +83 True 129 +84 True 12 +85 True 297 +86 True 295 +87 True 127 +88 True 208 +89 True 281 +90 True 265 +91 True 254 +92 True 122 +93 True 76 +94 True 237 +95 True 74 +96 True 65 +97 True 45 +98 True 90 +99 True 147 +100 True 189 +101 True 170 +102 True 207 +103 True 14 +104 True 307 +105 True 267 +106 True 111 +107 True 94 +108 True 306 +109 True 126 +110 True 269 +111 True 116 +112 True 140 +113 True 260 +114 True 201 +115 True 198 +116 True 155 +117 True 256 +118 True 214 +119 True 70 +120 True 304 +121 True 336 +122 True 201 +123 True 305 +124 True 301 +125 True 301 +126 True 338 +127 True 81 +128 True 256 +129 True 277 +130 True 237 +131 True 173 +132 True 228 +133 True 64 +134 True 52 +135 True 34 +136 True 333 +137 True 285 +138 True 132 +139 True 32 +140 True 275 +141 True 31 +142 True 244 +143 True 15 +144 True 54 +145 True 289 +146 True 186 +147 True 283 +148 True 333 +149 True 53 +150 True 26 +151 True 173 +152 True 19 +153 True 109 +154 True 138 +155 True 264 +156 True 293 +157 True 225 +158 True 150 +159 True 62 +160 True 350 +161 True 13 +162 True 341 +163 True 223 +164 True 177 +165 True 15 +166 True 202 +167 True 101 +168 True 203 +169 True 271 +170 True 305 +171 True 45 +172 True 322 +173 True 164 +174 True 213 +175 True 55 +176 True 143 +177 True 112 +178 True 266 +179 True 168 +180 True 9 +181 True 300 +182 True 249 +183 True 101 +184 True 55 +185 True 312 +186 True 181 +187 True 256 +188 True 27 +189 True 242 +190 True 210 +191 True 12 +192 True 203 +193 True 41 +194 True 205 +195 True 315 +196 True 94 +197 True 262 +198 True 316 +199 True 13 +200 True 94 +201 True 204 +202 True 245 +203 True 11 +204 True 238 +205 True 301 +206 True 219 +207 True 106 +208 True 253 +209 True 134 +210 True 262 +211 True 222 +212 True 82 +213 True 153 +214 True 122 +215 True 211 +216 True 49 +217 True 211 +218 True 176 +219 True 329 +220 True 8 |
| b |
| diff -r 000000000000 -r 6ea5a05a260a test-data/pp.filter_genes_dispersion.krumsiek11-seurat.h5ad |
| b |
| Binary file test-data/pp.filter_genes_dispersion.krumsiek11-seurat.h5ad has changed |
| b |
| diff -r 000000000000 -r 6ea5a05a260a test-data/pp.filter_genes_dispersion.per_gene.krumsiek11-cell_ranger.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/pp.filter_genes_dispersion.per_gene.krumsiek11-cell_ranger.tabular Mon Mar 04 10:15:02 2019 -0500 |
| b |
| @@ -0,0 +1,12 @@ + gene_subset means dispersions dispersions_norm +0 False 0.22807331 -1.513815 +1 False 0.27662647 -0.6374868 +2 False 0.12324284 -1.1931922 +3 True 0.10477218 -0.8270577 0.67448974 +4 True 0.08612139 -0.880823 0.67448974 +5 False 0.2751125 -0.6042374 +6 False 0.55053085 -1.5924454 +7 False 0.3306357 -0.91260546 +8 False 0.25766766 -0.86990273 +9 False 0.22937028 -0.7354343 +10 False 0.223133 -0.96748924 |
| b |
| diff -r 000000000000 -r 6ea5a05a260a test-data/pp.filter_genes_dispersion.per_gene.krumsiek11-seurat.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/pp.filter_genes_dispersion.per_gene.krumsiek11-seurat.tabular Mon Mar 04 10:15:02 2019 -0500 |
| b |
| @@ -0,0 +1,9 @@ +index means dispersions dispersions_norm +Fog1 0.12324284 -1.1931922 1.0 +EKLF 0.10477218 -0.8270577 0.70710677 +SCL 0.2751125 -0.6042374 0.707108 +Cebpa 0.55053085 -1.5924454 1.0 +Pu.1 0.3306357 -0.91260546 1.0 +cJun 0.25766766 -0.86990273 1.0 +EgrNab 0.22937028 -0.7354343 0.7071069 +Gfi1 0.223133 -0.96748924 1.0 |
| b |
| diff -r 000000000000 -r 6ea5a05a260a test-data/pp.log1p.krumsiek11.h5ad |
| b |
| Binary file test-data/pp.log1p.krumsiek11.h5ad has changed |
| b |
| diff -r 000000000000 -r 6ea5a05a260a test-data/pp.neighbors_gauss_braycurtis.recipe_weinreb17.paul15_subsample.h5ad |
| b |
| Binary file test-data/pp.neighbors_gauss_braycurtis.recipe_weinreb17.paul15_subsample.h5ad has changed |
| b |
| diff -r 000000000000 -r 6ea5a05a260a test-data/pp.neighbors_umap_euclidean.recipe_weinreb17.paul15_subsample.h5ad |
| b |
| Binary file test-data/pp.neighbors_umap_euclidean.recipe_weinreb17.paul15_subsample.h5ad has changed |
| b |
| diff -r 000000000000 -r 6ea5a05a260a test-data/pp.normalize_per_cell.krumsiek11.h5ad |
| b |
| Binary file test-data/pp.normalize_per_cell.krumsiek11.h5ad has changed |
| b |
| diff -r 000000000000 -r 6ea5a05a260a test-data/pp.normalize_per_cell.obs.krumsiek11.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/pp.normalize_per_cell.obs.krumsiek11.tabular Mon Mar 04 10:15:02 2019 -0500 |
| b |
| @@ -0,0 +1,641 @@ +index cell_type +0 progenitor +1 progenitor +2 progenitor +3 progenitor +4 progenitor +5 progenitor +6 progenitor +7 progenitor +8 progenitor +9 progenitor +10 progenitor +11 progenitor +12 progenitor +13 progenitor +14 progenitor +15 progenitor +16 progenitor +17 progenitor +18 progenitor +19 progenitor +20 progenitor +21 progenitor +22 progenitor +23 progenitor +24 progenitor +25 progenitor +26 progenitor +27 progenitor +28 progenitor +29 progenitor +30 progenitor +31 progenitor +32 progenitor +33 progenitor +34 progenitor +35 progenitor +36 progenitor +37 progenitor +38 progenitor +39 progenitor +40 progenitor +41 progenitor +42 progenitor +43 progenitor +44 progenitor +45 progenitor +46 progenitor +47 progenitor +48 progenitor +49 progenitor +50 progenitor +51 progenitor +52 progenitor +53 progenitor +54 progenitor +55 progenitor +56 progenitor +57 progenitor +58 progenitor +59 progenitor +60 progenitor +61 progenitor +62 progenitor +63 progenitor +64 progenitor +65 progenitor +66 progenitor +67 progenitor +68 progenitor +69 progenitor +70 progenitor +71 progenitor +72 progenitor +73 progenitor +74 progenitor +75 progenitor +76 progenitor +77 progenitor +78 progenitor +79 progenitor +80 Mo +81 Mo +82 Mo +83 Mo +84 Mo +85 Mo +86 Mo +87 Mo +88 Mo +89 Mo +90 Mo +91 Mo +92 Mo +93 Mo +94 Mo +95 Mo +96 Mo +97 Mo +98 Mo +99 Mo +100 Mo +101 Mo +102 Mo +103 Mo +104 Mo +105 Mo +106 Mo +107 Mo +108 Mo +109 Mo +110 Mo +111 Mo +112 Mo +113 Mo +114 Mo +115 Mo +116 Mo +117 Mo +118 Mo +119 Mo +120 Mo +121 Mo +122 Mo +123 Mo +124 Mo +125 Mo +126 Mo +127 Mo +128 Mo +129 Mo +130 Mo +131 Mo +132 Mo +133 Mo +134 Mo +135 Mo +136 Mo +137 Mo +138 Mo +139 Mo +140 Mo +141 Mo +142 Mo +143 Mo +144 Mo +145 Mo +146 Mo +147 Mo +148 Mo +149 Mo +150 Mo +151 Mo +152 Mo +153 Mo +154 Mo +155 Mo +156 Mo +157 Mo +158 Mo +159 Mo +0 progenitor +1 progenitor +2 progenitor +3 progenitor +4 progenitor +5 progenitor +6 progenitor +7 progenitor +8 progenitor +9 progenitor +10 progenitor +11 progenitor +12 progenitor +13 progenitor +14 progenitor +15 progenitor +16 progenitor +17 progenitor +18 progenitor +19 progenitor +20 progenitor +21 progenitor +22 progenitor +23 progenitor +24 progenitor +25 progenitor +26 progenitor +27 progenitor +28 progenitor +29 progenitor +30 progenitor +31 progenitor +32 progenitor +33 progenitor +34 progenitor +35 progenitor +36 progenitor +37 progenitor +38 progenitor +39 progenitor +40 progenitor +41 progenitor +42 progenitor +43 progenitor +44 progenitor +45 progenitor +46 progenitor +47 progenitor +48 progenitor +49 progenitor +50 progenitor +51 progenitor +52 progenitor +53 progenitor +54 progenitor +55 progenitor +56 progenitor +57 progenitor +58 progenitor +59 progenitor +60 progenitor +61 progenitor +62 progenitor +63 progenitor +64 progenitor +65 progenitor +66 progenitor +67 progenitor +68 progenitor +69 progenitor +70 progenitor +71 progenitor +72 progenitor +73 progenitor +74 progenitor +75 progenitor +76 progenitor +77 progenitor +78 progenitor +79 progenitor +80 Ery +81 Ery +82 Ery +83 Ery +84 Ery +85 Ery +86 Ery +87 Ery +88 Ery +89 Ery +90 Ery +91 Ery +92 Ery +93 Ery +94 Ery +95 Ery +96 Ery +97 Ery +98 Ery +99 Ery +100 Ery +101 Ery +102 Ery +103 Ery +104 Ery +105 Ery +106 Ery +107 Ery +108 Ery +109 Ery +110 Ery +111 Ery +112 Ery +113 Ery +114 Ery +115 Ery +116 Ery +117 Ery +118 Ery +119 Ery +120 Ery +121 Ery +122 Ery +123 Ery +124 Ery +125 Ery +126 Ery +127 Ery +128 Ery +129 Ery +130 Ery +131 Ery +132 Ery +133 Ery +134 Ery +135 Ery +136 Ery +137 Ery +138 Ery +139 Ery +140 Ery +141 Ery +142 Ery +143 Ery +144 Ery +145 Ery +146 Ery +147 Ery +148 Ery +149 Ery +150 Ery +151 Ery +152 Ery +153 Ery +154 Ery +155 Ery +156 Ery +157 Ery +158 Ery +159 Ery +0 progenitor +1 progenitor +2 progenitor +3 progenitor +4 progenitor +5 progenitor +6 progenitor +7 progenitor +8 progenitor +9 progenitor +10 progenitor +11 progenitor +12 progenitor +13 progenitor +14 progenitor +15 progenitor +16 progenitor +17 progenitor +18 progenitor +19 progenitor +20 progenitor +21 progenitor +22 progenitor +23 progenitor +24 progenitor +25 progenitor +26 progenitor +27 progenitor +28 progenitor +29 progenitor +30 progenitor +31 progenitor +32 progenitor +33 progenitor +34 progenitor +35 progenitor +36 progenitor +37 progenitor +38 progenitor +39 progenitor +40 progenitor +41 progenitor +42 progenitor +43 progenitor +44 progenitor +45 progenitor +46 progenitor +47 progenitor +48 progenitor +49 progenitor +50 progenitor +51 progenitor +52 progenitor +53 progenitor +54 progenitor +55 progenitor +56 progenitor +57 progenitor +58 progenitor +59 progenitor +60 progenitor +61 progenitor +62 progenitor +63 progenitor +64 progenitor +65 progenitor +66 progenitor +67 progenitor +68 progenitor +69 progenitor +70 progenitor +71 progenitor +72 progenitor +73 progenitor +74 progenitor +75 progenitor +76 progenitor +77 progenitor +78 progenitor +79 progenitor +80 Mk +81 Mk +82 Mk +83 Mk +84 Mk +85 Mk +86 Mk +87 Mk +88 Mk +89 Mk +90 Mk +91 Mk +92 Mk +93 Mk +94 Mk +95 Mk +96 Mk +97 Mk +98 Mk +99 Mk +100 Mk +101 Mk +102 Mk +103 Mk +104 Mk +105 Mk +106 Mk +107 Mk +108 Mk +109 Mk +110 Mk +111 Mk +112 Mk +113 Mk +114 Mk +115 Mk +116 Mk +117 Mk +118 Mk +119 Mk +120 Mk +121 Mk +122 Mk +123 Mk +124 Mk +125 Mk +126 Mk +127 Mk +128 Mk +129 Mk +130 Mk +131 Mk +132 Mk +133 Mk +134 Mk +135 Mk +136 Mk +137 Mk +138 Mk +139 Mk +140 Mk +141 Mk +142 Mk +143 Mk +144 Mk +145 Mk +146 Mk +147 Mk +148 Mk +149 Mk +150 Mk +151 Mk +152 Mk +153 Mk +154 Mk +155 Mk +156 Mk +157 Mk +158 Mk +159 Mk +0 progenitor +1 progenitor +2 progenitor +3 progenitor +4 progenitor +5 progenitor +6 progenitor +7 progenitor +8 progenitor +9 progenitor +10 progenitor +11 progenitor +12 progenitor +13 progenitor +14 progenitor +15 progenitor +16 progenitor +17 progenitor +18 progenitor +19 progenitor +20 progenitor +21 progenitor +22 progenitor +23 progenitor +24 progenitor +25 progenitor +26 progenitor +27 progenitor +28 progenitor +29 progenitor +30 progenitor +31 progenitor +32 progenitor +33 progenitor +34 progenitor +35 progenitor +36 progenitor +37 progenitor +38 progenitor +39 progenitor +40 progenitor +41 progenitor +42 progenitor +43 progenitor +44 progenitor +45 progenitor +46 progenitor +47 progenitor +48 progenitor +49 progenitor +50 progenitor +51 progenitor +52 progenitor +53 progenitor +54 progenitor +55 progenitor +56 progenitor +57 progenitor +58 progenitor +59 progenitor +60 progenitor +61 progenitor +62 progenitor +63 progenitor +64 progenitor +65 progenitor +66 progenitor +67 progenitor +68 progenitor +69 progenitor +70 progenitor +71 progenitor +72 progenitor +73 progenitor +74 progenitor +75 progenitor +76 progenitor +77 progenitor +78 progenitor +79 progenitor +80 Neu +81 Neu +82 Neu +83 Neu +84 Neu +85 Neu +86 Neu +87 Neu +88 Neu +89 Neu +90 Neu +91 Neu +92 Neu +93 Neu +94 Neu +95 Neu +96 Neu +97 Neu +98 Neu +99 Neu +100 Neu +101 Neu +102 Neu +103 Neu +104 Neu +105 Neu +106 Neu +107 Neu +108 Neu +109 Neu +110 Neu +111 Neu +112 Neu +113 Neu +114 Neu +115 Neu +116 Neu +117 Neu +118 Neu +119 Neu +120 Neu +121 Neu +122 Neu +123 Neu +124 Neu +125 Neu +126 Neu +127 Neu +128 Neu +129 Neu +130 Neu +131 Neu +132 Neu +133 Neu +134 Neu +135 Neu +136 Neu +137 Neu +138 Neu +139 Neu +140 Neu +141 Neu +142 Neu +143 Neu +144 Neu +145 Neu +146 Neu +147 Neu +148 Neu +149 Neu +150 Neu +151 Neu +152 Neu +153 Neu +154 Neu +155 Neu +156 Neu +157 Neu +158 Neu +159 Neu |
| b |
| diff -r 000000000000 -r 6ea5a05a260a test-data/pp.pca.krumsiek11.h5ad |
| b |
| Binary file test-data/pp.pca.krumsiek11.h5ad has changed |
| b |
| diff -r 000000000000 -r 6ea5a05a260a test-data/pp.pca.krumsiek11_chunk.h5ad |
| b |
| Binary file test-data/pp.pca.krumsiek11_chunk.h5ad has changed |
| b |
| diff -r 000000000000 -r 6ea5a05a260a test-data/pp.pca.variance.krumsiek11.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/pp.pca.variance.krumsiek11.tabular Mon Mar 04 10:15:02 2019 -0500 |
| b |
| @@ -0,0 +1,10 @@ +7.540945410728454590e-01 +2.517578899860382080e-01 +8.900784701108932495e-02 +4.575614631175994873e-02 +2.166538313031196594e-02 +5.896944552659988403e-03 +2.081273589283227921e-03 +1.173791475594043732e-03 +1.542696409160271287e-04 +3.281867248006165028e-05 |
| b |
| diff -r 000000000000 -r 6ea5a05a260a test-data/pp.recipe_seurat.recipe_zheng17.h5ad |
| b |
| Binary file test-data/pp.recipe_seurat.recipe_zheng17.h5ad has changed |
| b |
| diff -r 000000000000 -r 6ea5a05a260a test-data/pp.recipe_weinreb17.paul15_subsample.h5ad |
| b |
| Binary file test-data/pp.recipe_weinreb17.paul15_subsample.h5ad has changed |
| b |
| diff -r 000000000000 -r 6ea5a05a260a test-data/pp.recipe_zheng17.random-randint.h5ad |
| b |
| Binary file test-data/pp.recipe_zheng17.random-randint.h5ad has changed |
| b |
| diff -r 000000000000 -r 6ea5a05a260a test-data/pp.regress_out.krumsiek11.h5ad |
| b |
| Binary file test-data/pp.regress_out.krumsiek11.h5ad has changed |
| b |
| diff -r 000000000000 -r 6ea5a05a260a test-data/pp.scale.krumsiek11.h5ad |
| b |
| Binary file test-data/pp.scale.krumsiek11.h5ad has changed |
| b |
| diff -r 000000000000 -r 6ea5a05a260a test-data/pp.scale_max_value.krumsiek11.h5ad |
| b |
| Binary file test-data/pp.scale_max_value.krumsiek11.h5ad has changed |
| b |
| diff -r 000000000000 -r 6ea5a05a260a test-data/pp.sqrt.krumsiek11.h5ad |
| b |
| Binary file test-data/pp.sqrt.krumsiek11.h5ad has changed |
| b |
| diff -r 000000000000 -r 6ea5a05a260a test-data/pp.subsample.krumsiek11_fraction.h5ad |
| b |
| Binary file test-data/pp.subsample.krumsiek11_fraction.h5ad has changed |
| b |
| diff -r 000000000000 -r 6ea5a05a260a test-data/pp.subsample.krumsiek11_n_obs.h5ad |
| b |
| Binary file test-data/pp.subsample.krumsiek11_n_obs.h5ad has changed |
| b |
| diff -r 000000000000 -r 6ea5a05a260a test-data/random-randint.h5ad |
| b |
| Binary file test-data/random-randint.h5ad has changed |
| b |
| diff -r 000000000000 -r 6ea5a05a260a test-data/random.h5ad |
| b |
| Binary file test-data/random.h5ad has changed |
| b |
| diff -r 000000000000 -r 6ea5a05a260a test-data/tl.diffmap.neighbors_gauss_braycurtis.recipe_weinreb17.paul15_subsample.X_diffmap.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/tl.diffmap.neighbors_gauss_braycurtis.recipe_weinreb17.paul15_subsample.X_diffmap.tabular Mon Mar 04 10:15:02 2019 -0500 |
| b |
| b'@@ -0,0 +1,100 @@\n+1.006254479289054871e-01\t7.390013337135314941e-02\t5.162549763917922974e-02\t-6.088243797421455383e-02\t1.660361140966415405e-02\t2.669865079224109650e-02\t-1.013666391372680664e-01\t5.378784239292144775e-02\t2.008118629455566406e-01\t1.484276503324508667e-01\t1.083310469985008240e-01\t1.318635195493698120e-01\t1.997928470373153687e-01\t-7.899370044469833374e-02\t-2.425468564033508301e-01\n+9.916571527719497681e-02\t-6.192789599299430847e-02\t3.743748366832733154e-02\t5.766532197594642639e-02\t2.186784986406564713e-03\t-1.058542281389236450e-01\t5.377947166562080383e-02\t1.402157917618751526e-02\t1.486204266548156738e-01\t8.553525805473327637e-02\t2.134956121444702148e-01\t-9.449188411235809326e-02\t-9.736447781324386597e-02\t-6.411797553300857544e-02\t-3.109178543090820312e-01\n+1.063194051384925842e-01\t8.235514909029006958e-02\t9.153002500534057617e-02\t-1.288201361894607544e-01\t2.123118191957473755e-02\t-5.571385100483894348e-02\t4.388944245874881744e-03\t-1.907968819141387939e-01\t5.077145248651504517e-02\t-5.320586264133453369e-02\t-2.017502486705780029e-02\t2.888677455484867096e-02\t-3.507991880178451538e-02\t5.667190253734588623e-02\t7.913256995379924774e-03\n+9.840648621320724487e-02\t-4.607489332556724548e-02\t3.584916703402996063e-03\t1.064319070428609848e-02\t-1.083880066871643066e-01\t1.248296573758125305e-01\t6.351136416196823120e-02\t1.885401159524917603e-01\t-2.020059973001480103e-01\t3.631909489631652832e-01\t1.699842363595962524e-01\t1.017943695187568665e-01\t-1.385858207941055298e-01\t3.727469593286514282e-02\t8.702995628118515015e-02\n+1.002686843276023865e-01\t8.042127639055252075e-02\t-1.485065966844558716e-01\t-1.834145635366439819e-01\t1.185779422521591187e-01\t-4.452232271432876587e-03\t2.401492185890674591e-02\t1.709450007183477283e-04\t-1.044583246111869812e-01\t1.082587465643882751e-01\t8.498968929052352905e-02\t1.078867260366678238e-02\t1.678988523781299591e-02\t-4.863050952553749084e-02\t-8.437795564532279968e-03\n+1.039626300334930420e-01\t6.898555904626846313e-02\t-5.245065316557884216e-02\t-1.401370912790298462e-01\t1.724163144826889038e-01\t-9.417925775051116943e-02\t5.670287460088729858e-02\t-2.294020541012287140e-02\t-1.041278913617134094e-01\t-4.751206189393997192e-02\t-2.486055344343185425e-02\t1.906321793794631958e-01\t-1.133706346154212952e-01\t1.018952578306198120e-01\t-1.696813404560089111e-01\n+1.031595841050148010e-01\t6.644981354475021362e-02\t-3.434765338897705078e-02\t-8.121536672115325928e-02\t-2.303110063076019287e-01\t6.845026742666959763e-03\t-3.113305754959583282e-02\t3.572509065270423889e-02\t-2.340330332517623901e-01\t1.681309342384338379e-01\t2.042572945356369019e-01\t-2.152139544486999512e-01\t3.323959186673164368e-02\t-1.992796063423156738e-01\t1.612142026424407959e-01\n+1.063378602266311646e-01\t9.444754570722579956e-02\t1.147621273994445801e-01\t-1.788049340248107910e-01\t1.663699001073837280e-01\t-1.299377232789993286e-01\t9.099455177783966064e-02\t8.901253342628479004e-02\t-3.782828152179718018e-02\t1.340985000133514404e-01\t-1.110952645540237427e-01\t-1.353431493043899536e-01\t9.196916222572326660e-02\t-5.004190653562545776e-02\t1.283620446920394897e-01\n+1.019066423177719116e-01\t3.868932276964187622e-02\t-5.681320559233427048e-03\t2.885684370994567871e-02\t-1.618600785732269287e-01\t-7.793435454368591309e-02\t-6.321301311254501343e-02\t-7.030926644802093506e-02\t-8.451142162084579468e-02\t1.784774512052536011e-01\t-5.302700772881507874e-02\t2.233742922544479370e-02\t-8.568169549107551575e-03\t-3.328817337751388550e-02\t-2.190946601331233978e-02\n+1.055724918842315674e-01\t6.597422808408737183e-02\t1.207857206463813782e-01\t-1.769655644893646240e-01\t-1.941676251590251923e-02\t-2.537060342729091644e-02\t2.017348445951938629e-02\t2.019873559474945068e-01\t2.603957951068878174e-01\t-8.517616987228393555e-02\t1.920531690120697021e-01\t3.013696968555450439e-01\t1.285752207040786743e-01\t-6.937998533248901367e-02\t2.583270706236362457e-02\n+1.013405695557594299e-01\t7.315808534622192383e-02\t-4.366664588451385498e-02\t2.623320743441581726e-02\t-1.268581300973892212e-01\t-9.996589273214340210e-02\t3.80'..b'926277161e-02\t6.935269385576248169e-02\t5.418083444237709045e-02\t-2.927818335592746735e-02\t2.737504616379737854e-02\t6.675768643617630005e-03\t-4.358346015214920044e-02\n+1.045850887894630432e-01\t3.966004028916358948e-02\t7.888220995664596558e-02\t1.084793508052825928e-01\t-3.825098276138305664e-02\t5.556414648890495300e-02\t-2.386018633842468262e-03\t-1.735868491232395172e-02\t1.626232713460922241e-01\t-3.189559327438473701e-03\t-3.677500039339065552e-02\t-1.077032759785652161e-01\t-6.530553102493286133e-02\t-1.181415840983390808e-01\t2.054665982723236084e-01\n+1.013580858707427979e-01\t6.717060506343841553e-02\t-7.871925085783004761e-02\t-4.536754917353391647e-03\t-8.628232032060623169e-02\t-4.364237934350967407e-02\t5.463447421789169312e-02\t7.559294998645782471e-02\t1.829659007489681244e-02\t-3.810231760144233704e-02\t1.445978041738271713e-02\t-1.330154389142990112e-01\t7.491165399551391602e-02\t-5.850773304700851440e-02\t5.279816687107086182e-03\n+1.007874831557273865e-01\t-6.051312014460563660e-02\t-2.818964421749114990e-03\t1.158334836363792419e-01\t-6.604961305856704712e-02\t-6.636043637990951538e-02\t3.605647683143615723e-01\t6.230036914348602295e-02\t1.247871741652488708e-01\t4.024268593639135361e-03\t-4.460835456848144531e-02\t1.964040845632553101e-01\t1.187151372432708740e-01\t2.093635946512222290e-01\t2.515807449817657471e-01\n+1.040665134787559509e-01\t7.813188433647155762e-02\t1.352884173393249512e-01\t-9.691929072141647339e-02\t2.978404052555561066e-02\t-6.218590214848518372e-02\t3.118260763585567474e-02\t2.100257873535156250e-01\t5.309388414025306702e-02\t-3.683280944824218750e-02\t1.081678271293640137e-01\t1.159011572599411011e-01\t-9.071216732263565063e-02\t1.454317569732666016e-01\t1.560889184474945068e-02\n+9.596666693687438965e-02\t-1.235919669270515442e-01\t-6.143675185739994049e-03\t4.618058353662490845e-02\t-4.854806885123252869e-02\t-1.566148698329925537e-01\t1.086631417274475098e-01\t-5.864029750227928162e-02\t7.967603951692581177e-02\t-4.821031168103218079e-02\t-7.968238554894924164e-03\t-5.616628099232912064e-03\t-7.662835996598005295e-03\t-5.304025113582611084e-02\t-9.814745932817459106e-02\n+9.450878947973251343e-02\t-1.617153137922286987e-01\t-1.475114375352859497e-02\t-3.400534763932228088e-02\t3.202979266643524170e-02\t-7.523473352193832397e-03\t-7.037699967622756958e-02\t5.858044326305389404e-02\t-2.339935861527919769e-02\t6.765121361240744591e-05\t-7.621700875461101532e-03\t-2.569160657003521919e-03\t1.386285480111837387e-02\t-9.449950885027647018e-04\t-9.074879810214042664e-03\n+9.348812699317932129e-02\t-1.875597685575485229e-01\t-1.796119287610054016e-02\t-2.141974493861198425e-02\t2.915703505277633667e-02\t-5.883788317441940308e-02\t-1.005370840430259705e-01\t3.347435966134071350e-02\t2.262158133089542389e-02\t1.751536689698696136e-02\t3.964411094784736633e-02\t-3.229109104722738266e-03\t-1.950366050004959106e-02\t1.035222597420215607e-02\t-1.544480863958597183e-02\n+9.449574351310729980e-02\t-1.709264367818832397e-01\t4.125457257032394409e-03\t-6.873404979705810547e-02\t4.397033154964447021e-02\t1.867942214012145996e-01\t-1.137310042977333069e-01\t6.536182016134262085e-02\t-8.733030408620834351e-02\t4.486828297376632690e-02\t6.879048049449920654e-02\t3.395766764879226685e-02\t-1.334057748317718506e-01\t-3.880335018038749695e-02\t5.785062164068222046e-02\n+9.526924788951873779e-02\t-1.083553209900856018e-01\t1.990574225783348083e-02\t1.783852465450763702e-02\t-5.172537639737129211e-02\t-1.314793080091476440e-01\t-3.332496806979179382e-02\t-1.304124593734741211e-01\t7.114066183567047119e-02\t4.942291602492332458e-02\t1.143850944936275482e-02\t3.503248840570449829e-02\t8.114560507237911224e-03\t2.840096876025199890e-02\t6.378748267889022827e-02\n+1.035511195659637451e-01\t7.710250467061996460e-02\t5.883126333355903625e-02\t-1.181510612368583679e-01\t-1.791930794715881348e-01\t-2.050231397151947021e-02\t-4.374536871910095215e-02\t2.246104925870895386e-01\t1.195801421999931335e-02\t-1.478822380304336548e-01\t-9.886784851551055908e-02\t-9.984883666038513184e-02\t-6.099858880043029785e-02\t8.420736342668533325e-02\t-9.065923094749450684e-02\n' |
| b |
| diff -r 000000000000 -r 6ea5a05a260a test-data/tl.diffmap.neighbors_gauss_braycurtis.recipe_weinreb17.paul15_subsample.h5ad |
| b |
| Binary file test-data/tl.diffmap.neighbors_gauss_braycurtis.recipe_weinreb17.paul15_subsample.h5ad has changed |
| b |
| diff -r 000000000000 -r 6ea5a05a260a test-data/tl.dpt.diffmap.neighbors_gauss_braycurtis.recipe_weinreb17.paul15_subsample.h5ad |
| b |
| Binary file test-data/tl.dpt.diffmap.neighbors_gauss_braycurtis.recipe_weinreb17.paul15_subsample.h5ad has changed |
| b |
| diff -r 000000000000 -r 6ea5a05a260a test-data/tl.dpt.diffmap.neighbors_gauss_braycurtis.recipe_weinreb17.paul15_subsample.obs.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/tl.dpt.diffmap.neighbors_gauss_braycurtis.recipe_weinreb17.paul15_subsample.obs.tabular Mon Mar 04 10:15:02 2019 -0500 |
| b |
| @@ -0,0 +1,101 @@ +index paul15_clusters dpt_groups dpt_order dpt_order_indices +578 13Baso 2 53 27 +2242 3Ery 1 30 46 +2690 10GMP 2 66 45 +70 5Ery 1 32 65 +758 15Mo 2 67 8 +465 16Neu 2 68 80 +245 16Neu 2 69 87 +2172 10GMP 2 70 90 +2680 10GMP 0 4 36 +1790 7MEP 2 71 59 +855 11DC 2 72 82 +2721 10GMP 2 73 30 +104 2Ery 1 38 62 +1106 2Ery 1 40 32 +2367 15Mo 3 93 35 +124 2Ery 1 41 37 +2477 8Mk 2 74 31 +1968 2Ery 1 42 78 +563 1Ery 1 43 28 +276 2Ery 1 44 56 +192 16Neu 2 75 42 +2409 2Ery 1 45 44 +2054 15Mo 3 95 75 +720 8Mk 2 76 48 +2225 14Mo 3 97 98 +878 6Ery 1 29 54 +156 7MEP 2 77 79 +1244 8Mk 0 0 40 +10 2Ery 1 18 83 +1108 6Ery 2 65 25 +353 5Ery 1 11 1 +182 5Ery 1 16 97 +2053 3Ery 1 13 3 +2291 16Neu 3 92 96 +2056 10GMP 2 79 95 +1047 2Ery 1 14 94 +1947 14Mo 0 8 92 +1390 3Ery 1 15 60 +2317 14Mo 2 90 12 +2348 11DC 2 82 69 +953 5Ery 1 27 13 +628 9GMP 2 83 15 +2691 5Ery 1 20 17 +1499 16Neu 3 96 18 +1083 2Ery 1 21 19 +831 14Mo 0 2 21 +15 7MEP 0 1 86 +2005 7MEP 2 87 66 +1662 3Ery 1 23 84 +2457 7MEP 2 64 89 +757 7MEP 2 81 70 +1642 14Mo 2 91 68 +2520 10GMP 2 89 67 +1393 7MEP 2 88 0 +2170 6Ery 1 25 73 +988 14Mo 2 86 76 +1338 2Ery 1 19 77 +2189 16Neu 2 85 81 +446 13Baso 2 84 85 +2276 14Mo 0 9 88 +317 2Ery 1 37 91 +1540 16Neu 3 99 93 +2164 4Ery 1 12 72 +227 15Mo 2 78 64 +906 12Baso 2 63 49 +716 15Mo 0 3 29 +912 14Mo 1 47 2 +2688 11DC 2 52 4 +1678 7MEP 2 51 5 +1063 6Ery 1 39 6 +1041 5Ery 1 50 7 +2279 15Mo 3 98 9 +558 13Baso 2 62 10 +2196 14Mo 2 54 11 +1270 13Baso 3 94 16 +2259 3Ery 1 22 20 +2410 13Baso 2 55 23 +886 7MEP 2 56 26 +2072 13Baso 1 17 63 +443 5Ery 1 26 34 +910 13Baso 0 5 99 +2608 15Mo 2 57 50 +2645 1Ery 1 10 39 +616 6Ery 1 28 41 +1866 2Ery 1 48 58 +923 7MEP 2 58 57 +1716 4Ery 1 46 55 +2476 11DC 0 6 47 +1872 10GMP 2 59 53 +1009 4Ery 1 49 52 +1680 6Ery 0 7 38 +1490 14Mo 2 60 51 +1454 2Ery 1 36 33 +2580 9GMP 2 61 14 +958 1Ery 1 35 74 +2626 2Ery 1 34 22 +1677 3Ery 1 33 43 +982 4Ery 1 31 24 +202 2Ery 1 24 71 +891 10GMP 2 80 61 |
| b |
| diff -r 000000000000 -r 6ea5a05a260a test-data/tl.dpt.neighbors.paul15_gauss_braycurtis.obs.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/tl.dpt.neighbors.paul15_gauss_braycurtis.obs.tabular Mon Mar 04 10:15:02 2019 -0500 |
| b |
| b'@@ -0,0 +1,2731 @@\n+index\tpaul15_clusters\tdpt_pseudotime\tdpt_groups\tdpt_order\tdpt_order_indices\n+0\t7MEP\t0.077775456\t1\t172\t404\n+1\t15Mo\t0.70791066\t2\t2592\t1876\n+2\t3Ery\t0.9299172\t1\t1309\t2408\n+3\t15Mo\t0.6765072\t2\t2406\t1880\n+4\t3Ery\t0.86704516\t1\t1154\t2098\n+5\t15Mo\t0.58440965\t2\t1808\t823\n+6\t4Ery\t0.60054153\t1\t688\t1149\n+7\t2Ery\t0.43734095\t1\t539\t2385\n+8\t3Ery\t0.2407884\t1\t367\t2384\n+9\t2Ery\t0.8557937\t1\t1110\t155\n+10\t2Ery\t0.8691475\t1\t1164\t2372\n+11\t17Neu\t0.30127475\t2\t1456\t2365\n+12\t14Mo\t0.63893527\t2\t2068\t164\n+13\t13Baso\t0.5479835\t2\t1748\t607\n+14\t3Ery\t0.8603202\t1\t1134\t167\n+15\t7MEP\t0.117413916\t1\t270\t1172\n+16\t3Ery\t0.6879372\t1\t786\t1908\n+17\t3Ery\t0.84132445\t1\t1055\t805\n+18\t2Ery\t0.8558495\t1\t1111\t2413\n+19\t8Mk\t0.1685136\t0\t98\t2417\n+20\t3Ery\t0.27082652\t1\t399\t1126\n+21\t9GMP\t0.35508415\t2\t1510\t2436\n+22\t8Mk\t0.12326076\t0\t100\t1815\n+23\t10GMP\t0.36161897\t2\t1515\t1616\n+24\t15Mo\t0.65855885\t2\t2259\t2511\n+25\t16Neu\t0.6648798\t2\t2312\t438\n+26\t4Ery\t0.7767835\t1\t889\t437\n+27\t13Baso\t0.411375\t2\t1588\t1607\n+28\t17Neu\t0.2787515\t2\t1438\t1089\n+29\t3Ery\t0.7026065\t1\t798\t2475\n+30\t2Ery\t0.78192663\t1\t899\t614\n+31\t3Ery\t0.4758986\t1\t578\t112\n+32\t5Ery\t0.52930063\t1\t627\t851\n+33\t3Ery\t0.5440802\t1\t638\t115\n+34\t13Baso\t0.5579254\t2\t1766\t2457\n+35\t1Ery\t0.9610762\t1\t1324\t423\n+36\t3Ery\t0.94298\t1\t1317\t1109\n+37\t6Ery\t0.35788366\t1\t471\t2452\n+38\t15Mo\t0.73092824\t2\t2657\t1858\n+39\t3Ery\t0.47530073\t1\t577\t1117\n+40\t3Ery\t0.8309953\t1\t1021\t1843\n+41\t14Mo\t0.64247084\t2\t2108\t384\n+42\t19Lymph\t0.4615774\t0\t113\t2323\n+43\t12Baso\t0.3523068\t2\t1509\t185\n+44\t3Ery\t0.8736262\t1\t1184\t1299\n+45\t14Mo\t0.64636815\t2\t2144\t2032\n+46\t6Ery\t0.41744366\t1\t524\t1306\n+47\t4Ery\t0.7252952\t1\t817\t261\n+48\t7MEP\t0.2547727\t2\t1422\t2154\n+49\t2Ery\t0.8350906\t1\t1032\t723\n+50\t13Baso\t0.36504018\t2\t1520\t2051\n+51\t14Mo\t0.66908467\t2\t2351\t720\n+52\t6Ery\t0.26223817\t1\t393\t737\n+53\t18Eos\t0.3815021\t2\t1544\t1393\n+54\t4Ery\t0.8454671\t1\t1065\t718\n+55\t3Ery\t0.7204466\t1\t813\t715\n+56\t3Ery\t0.624237\t1\t720\t308\n+57\t14Mo\t0.63932437\t2\t2076\t1384\n+58\t2Ery\t0.84006816\t1\t1050\t1378\n+59\t13Baso\t0.6566314\t2\t2235\t1348\n+60\t2Ery\t0.85520875\t1\t1106\t1370\n+61\t13Baso\t0.6836325\t2\t2458\t1360\n+62\t13Baso\t0.6240188\t2\t1957\t2136\n+63\t14Mo\t0.6315316\t2\t2004\t2522\n+64\t7MEP\t0.12562352\t0\t94\t2172\n+65\t7MEP\t0.20317915\t1\t333\t2025\n+66\t7MEP\t0.14576882\t2\t1346\t793\n+67\t10GMP\t0.4374045\t2\t1628\t1505\n+68\t12Baso\t0.35526624\t2\t1511\t2293\n+69\t6Ery\t0.15430509\t1\t295\t1484\n+70\t5Ery\t0.29059684\t1\t421\t636\n+71\t5Ery\t0.41076174\t1\t516\t1222\n+72\t14Mo\t0.63960767\t2\t2078\t2269\n+73\t4Ery\t0.820214\t1\t994\t1238\n+74\t16Neu\t0.6670669\t2\t2332\t248\n+75\t16Neu\t0.6509542\t2\t2187\t1244\n+76\t3Ery\t0.66913307\t1\t766\t1457\n+77\t2Ery\t0.89367026\t1\t1250\t1455\n+78\t6Ery\t0.76215255\t1\t863\t1265\n+79\t13Baso\t0.59909\t2\t1840\t229\n+80\t13Baso\t0.45156288\t2\t1649\t2221\n+81\t10GMP\t0.49630007\t2\t1711\t2005\n+82\t14Mo\t0.6566849\t2\t2236\t1280\n+83\t5Ery\t0.45687908\t1\t559\t743\n+84\t7MEP\t0.14249937\t0\t127\t350\n+85\t7MEP\t0.0928669\t1\t216\t2540\n+86\t5Ery\t0.6481682\t1\t746\t2097\n+87\t6Ery\t0.26217386\t1\t392\t1654\n+88\t2Ery\t0.8884944\t1\t1232\t499\n+89\t10GMP\t0.07816703\t1\t173\t2564\n+90\t10GMP\t0.36928764\t2\t1526\t2687\n+91\t2Ery\t0.85090935\t1\t1086\t1651\n+92\t7MEP\t0.2221476\t2\t1399\t890\n+93\t6Ery\t0.22915362\t1\t356\t1726\n+94\t7MEP\t0.08779579\t1\t199\t64\n+95\t14Mo\t0.6131882\t2\t1902\t961\n+96\t16Neu\t0.6578041\t2\t2246\t1790\n+97\t10GMP\t0.43475908\t2\t1624\t1787\n+98\t3Ery\t0.79592675\t1\t927\t19\n+99\t3Ery\t0.8079216\t1\t959\t2592\n+100\t13Baso\t0.6605006\t2\t2280\t22\n+101\t1Ery\t1.0\t1\t1331\t523\n+102\t14Mo\t0.6370637\t2\t2050\t541\n+103\t15Mo\t0.7214093\t2\t2628\t1738\n+104\t2Ery\t0.73762625\t1\t832\t540\n+105\t5Ery\t0.21692096\t1\t344\t474\n+106\t2Ery\t0.8745584\t1\t1190\t2611\n+107\t5Ery\t0.30303305\t1\t430\t1774\n+108\t3Ery\t0.87296826\t1\t1179\t2661\n+109\t14Mo\t0.58798885\t2\t1815\t2659\n+110\t10GMP\t0.44662797\t2\t1644\t922\n+111\t2Ery\t0.8643726\t1\t1145\t525\n+112\t7MEP\t0.14947182\t0\t31\t974\n+113\t4Ery\t0.7285211\t1\t823\t42\n+114\t9GMP\t0.40913528\t2\t1585\t993\n+115\t7MEP\t0.13643783\t0\t33\t1630\n+116\t3Ery\t0.85794955\t1\t1122\t2631\n+117\t16Neu\t0.7009699\t2\t2561\t1034\n+118\t11DC\t0.5372636\t3\t2701\t1647\n+119\t10GMP\t0.37033108\t2\t1531\t1681\n+120\t6Ery\t0.32231367\t1\t446\t2713\n+121\t3Ery\t0.2562019\t1\t387\t452\n+122\t2Ery\t0.8032558\t1\t947\t2718\n+123\t5Ery\t0.79876626\t1\t935\t2707\n+124\t2Ery\t0.8192419\t1\t992\t2708\n+125\t2Ery\t0.80044454\t1\t'..b'+2610\t4Ery\t0.48178568\t1\t584\t1541\n+2611\t8Mk\t0.1514135\t0\t106\t1751\n+2612\t6Ery\t0.0745854\t1\t164\t2437\n+2613\t13Baso\t0.5688611\t2\t1781\t1863\n+2614\t13Baso\t0.6075742\t2\t1870\t205\n+2615\t5Ery\t0.40751126\t1\t511\t1591\n+2616\t10GMP\t0.35635096\t2\t1512\t2628\n+2617\t10GMP\t0.06013551\t1\t141\t2699\n+2618\t10GMP\t0.4497829\t2\t1647\t2374\n+2619\t2Ery\t0.6560231\t1\t751\t691\n+2620\t11DC\t0.82389486\t3\t2725\t815\n+2621\t16Neu\t0.70278895\t2\t2571\t1459\n+2622\t14Mo\t0.6140961\t2\t1909\t416\n+2623\t5Ery\t0.35220554\t1\t468\t2064\n+2624\t10GMP\t0.4581429\t2\t1658\t2702\n+2625\t6Ery\t0.2331504\t1\t363\t903\n+2626\t2Ery\t0.8517103\t1\t1089\t2556\n+2627\t10GMP\t0.5886404\t2\t1816\t990\n+2628\t15Mo\t0.71380967\t2\t2616\t103\n+2629\t16Neu\t0.7658805\t2\t2690\t129\n+2630\t6Ery\t0.10605643\t1\t249\t1421\n+2631\t19Lymph\t0.49200097\t0\t116\t2291\n+2632\t10GMP\t0.4024464\t2\t1575\t2701\n+2633\t15Mo\t0.74645966\t2\t2672\t245\n+2634\t13Baso\t0.6655569\t2\t2318\t914\n+2635\t5Ery\t0.27344576\t1\t401\t2698\n+2636\t7MEP\t0.0952574\t1\t225\t2432\n+2637\t4Ery\t0.5201689\t1\t620\t1844\n+2638\t7MEP\t0.20242327\t2\t1386\t1820\n+2639\t3Ery\t0.34670848\t1\t462\t1137\n+2640\t19Lymph\t0.39383155\t2\t1558\t2367\n+2641\t13Baso\t0.64991057\t2\t2177\t1010\n+2642\t13Baso\t0.60973185\t2\t1877\t1096\n+2643\t13Baso\t0.5230509\t2\t1727\t1375\n+2644\t3Ery\t0.7968286\t1\t931\t548\n+2645\t1Ery\t0.90491605\t1\t1280\t141\n+2646\t15Mo\t0.680559\t2\t2438\t2654\n+2647\t8Mk\t0.19091079\t2\t1375\t2041\n+2648\t7MEP\t0.16938637\t2\t1358\t2594\n+2649\t7MEP\t0.09380821\t1\t222\t235\n+2650\t13Baso\t0.51128185\t2\t1720\t585\n+2651\t13Baso\t0.610333\t2\t1882\t465\n+2652\t5Ery\t0.46644995\t1\t570\t2572\n+2653\t6Ery\t0.081108525\t1\t180\t537\n+2654\t15Mo\t0.7258329\t2\t2646\t2209\n+2655\t13Baso\t0.65495956\t2\t2223\t2414\n+2656\t14Mo\t0.70919186\t2\t2597\t1070\n+2657\t10GMP\t0.024275031\t1\t134\t38\n+2658\t13Baso\t0.6201747\t2\t1934\t2608\n+2659\t7MEP\t0.16126071\t0\t109\t2575\n+2660\t15Mo\t0.6923601\t2\t2510\t567\n+2661\t8Mk\t0.12896974\t0\t108\t348\n+2662\t9GMP\t0.44657716\t2\t1643\t697\n+2663\t4Ery\t0.40954873\t1\t514\t2532\n+2664\t17Neu\t0.27121463\t2\t1432\t986\n+2665\t2Ery\t0.7420347\t1\t843\t2692\n+2666\t14Mo\t0.66429305\t2\t2307\t1825\n+2667\t15Mo\t0.6961924\t2\t2530\t593\n+2668\t14Mo\t0.6633796\t2\t2301\t2071\n+2669\t6Ery\t0.29194444\t1\t422\t1202\n+2670\t6Ery\t0.1773625\t1\t315\t534\n+2671\t10GMP\t0.44642723\t2\t1642\t1918\n+2672\t6Ery\t0.093622796\t1\t220\t2633\n+2673\t13Baso\t0.57497\t2\t1790\t2193\n+2674\t6Ery\t0.08036224\t1\t178\t2343\n+2675\t12Baso\t0.46036804\t2\t1661\t2401\n+2676\t3Ery\t0.7683511\t1\t876\t1234\n+2677\t13Baso\t0.60261667\t2\t1846\t476\n+2678\t13Baso\t0.6276549\t2\t1974\t937\n+2679\t16Neu\t0.6842092\t2\t2462\t2686\n+2680\t10GMP\t0.5541122\t2\t1756\t2491\n+2681\t16Neu\t0.7632191\t2\t2688\t2390\n+2682\t13Baso\t0.6525333\t2\t2194\t451\n+2683\t5Ery\t0.3786639\t1\t484\t622\n+2684\t2Ery\t0.8525614\t1\t1093\t784\n+2685\t9GMP\t0.2187171\t2\t1396\t1952\n+2686\t16Neu\t0.7529708\t2\t2679\t458\n+2687\t8Mk\t0.10772686\t0\t90\t2526\n+2688\t11DC\t0.7538068\t3\t2709\t2681\n+2689\t13Baso\t0.5315107\t2\t1737\t483\n+2690\t10GMP\t0.4498889\t2\t1648\t2629\n+2691\t5Ery\t0.3065879\t1\t432\t675\n+2692\t15Mo\t0.73867893\t2\t2665\t2724\n+2693\t13Baso\t0.65786403\t2\t2247\t1770\n+2694\t9GMP\t0.33484194\t2\t1495\t489\n+2695\t14Mo\t0.6684571\t2\t2345\t517\n+2696\t13Baso\t0.48865384\t2\t1703\t1334\n+2697\t14Mo\t0.6743835\t2\t2392\t596\n+2698\t15Mo\t0.7228256\t2\t2635\t2566\n+2699\t15Mo\t0.7144696\t2\t2617\t2484\n+2700\t10GMP\t0.396035\t2\t1560\t1090\n+2701\t15Mo\t0.7221009\t2\t2632\t118\n+2702\t16Neu\t0.7181373\t2\t2624\t1595\n+2703\t6Ery\t0.28456205\t1\t415\t612\n+2704\t2Ery\t0.8019648\t1\t945\t1501\n+2705\t13Baso\t0.6341026\t2\t2020\t940\n+2706\t5Ery\t0.15244874\t1\t294\t855\n+2707\t7MEP\t0.15042938\t0\t123\t1798\n+2708\t19Lymph\t0.4686537\t0\t124\t417\n+2709\t6Ery\t0.18361242\t1\t321\t2688\n+2710\t13Baso\t0.6592802\t2\t2268\t1136\n+2711\t2Ery\t0.8232841\t1\t1001\t1672\n+2712\t11DC\t0.83255297\t3\t2728\t2348\n+2713\t7MEP\t0.15196408\t0\t120\t1871\n+2714\t13Baso\t0.5522318\t2\t1752\t401\n+2715\t2Ery\t0.63822633\t1\t735\t967\n+2716\t14Mo\t0.67126095\t2\t2366\t2406\n+2717\t13Baso\t0.66159946\t2\t2285\t501\n+2718\t8Mk\t0.1306417\t0\t122\t651\n+2719\t13Baso\t0.49483874\t2\t1709\t1687\n+2720\t7MEP\t0.1357271\t2\t1339\t801\n+2721\t10GMP\t0.41721123\t2\t1599\t291\n+2722\t10GMP\t0.5053347\t2\t1717\t2350\n+2723\t14Mo\t0.6557509\t2\t2228\t2109\n+2724\t16Neu\t0.7669956\t2\t2692\t1326\n+2725\t2Ery\t0.70807374\t1\t806\t2620\n+2726\t13Baso\t0.6412319\t2\t2096\t646\n+2727\t7MEP\t0.09423482\t1\t224\t1139\n+2728\t15Mo\t0.64149666\t2\t2099\t2712\n+2729\t3Ery\t0.77763766\t1\t892\t2476\n' |
| b |
| diff -r 000000000000 -r 6ea5a05a260a test-data/tl.louvain.neighbors_gauss_braycurtis.recipe_weinreb17.paul15_subsample.h5ad |
| b |
| Binary file test-data/tl.louvain.neighbors_gauss_braycurtis.recipe_weinreb17.paul15_subsample.h5ad has changed |
| b |
| diff -r 000000000000 -r 6ea5a05a260a test-data/tl.paga.neighbors_gauss_braycurtis.recipe_weinreb17.paul15_subsample.h5ad |
| b |
| Binary file test-data/tl.paga.neighbors_gauss_braycurtis.recipe_weinreb17.paul15_subsample.h5ad has changed |
| b |
| diff -r 000000000000 -r 6ea5a05a260a test-data/tl.pca.krumsiek11.h5ad |
| b |
| Binary file test-data/tl.pca.krumsiek11.h5ad has changed |
| b |
| diff -r 000000000000 -r 6ea5a05a260a test-data/tl.pca.variance_ratio.krumsiek11.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/tl.pca.variance_ratio.krumsiek11.tabular Mon Mar 04 10:15:02 2019 -0500 |
| b |
| @@ -0,0 +1,10 @@ +6.436238884925842285e-01 +2.148767709732055664e-01 +7.596869766712188721e-02 +3.905308619141578674e-02 +1.849153265357017517e-02 +5.033073481172323227e-03 +1.776377670466899872e-03 +1.001837081275880337e-03 +1.316703710472211242e-04 +2.801087975967675447e-05 |
| b |
| diff -r 000000000000 -r 6ea5a05a260a test-data/tl.rank_genes_groups.krumsiek11.h5ad |
| b |
| Binary file test-data/tl.rank_genes_groups.krumsiek11.h5ad has changed |
| b |
| diff -r 000000000000 -r 6ea5a05a260a test-data/tl.score_genes.krumsiek11.h5ad |
| b |
| Binary file test-data/tl.score_genes.krumsiek11.h5ad has changed |
| b |
| diff -r 000000000000 -r 6ea5a05a260a test-data/tl.score_genes.krumsiek11.obs.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/tl.score_genes.krumsiek11.obs.tabular Mon Mar 04 10:15:02 2019 -0500 |
| b |
| b'@@ -0,0 +1,641 @@\n+index\tcell_type\tscore\n+0\tprogenitor\t\n+1\tprogenitor\t\n+2\tprogenitor\t\n+3\tprogenitor\t\n+4\tprogenitor\t\n+5\tprogenitor\t\n+6\tprogenitor\t\n+7\tprogenitor\t\n+8\tprogenitor\t\n+9\tprogenitor\t\n+10\tprogenitor\t\n+11\tprogenitor\t\n+12\tprogenitor\t\n+13\tprogenitor\t\n+14\tprogenitor\t\n+15\tprogenitor\t\n+16\tprogenitor\t\n+17\tprogenitor\t\n+18\tprogenitor\t\n+19\tprogenitor\t\n+20\tprogenitor\t\n+21\tprogenitor\t\n+22\tprogenitor\t\n+23\tprogenitor\t\n+24\tprogenitor\t\n+25\tprogenitor\t\n+26\tprogenitor\t\n+27\tprogenitor\t\n+28\tprogenitor\t\n+29\tprogenitor\t\n+30\tprogenitor\t\n+31\tprogenitor\t\n+32\tprogenitor\t\n+33\tprogenitor\t\n+34\tprogenitor\t\n+35\tprogenitor\t\n+36\tprogenitor\t\n+37\tprogenitor\t\n+38\tprogenitor\t\n+39\tprogenitor\t\n+40\tprogenitor\t\n+41\tprogenitor\t\n+42\tprogenitor\t\n+43\tprogenitor\t\n+44\tprogenitor\t\n+45\tprogenitor\t\n+46\tprogenitor\t\n+47\tprogenitor\t\n+48\tprogenitor\t\n+49\tprogenitor\t\n+50\tprogenitor\t\n+51\tprogenitor\t\n+52\tprogenitor\t\n+53\tprogenitor\t\n+54\tprogenitor\t\n+55\tprogenitor\t\n+56\tprogenitor\t\n+57\tprogenitor\t\n+58\tprogenitor\t\n+59\tprogenitor\t\n+60\tprogenitor\t\n+61\tprogenitor\t\n+62\tprogenitor\t\n+63\tprogenitor\t\n+64\tprogenitor\t\n+65\tprogenitor\t\n+66\tprogenitor\t\n+67\tprogenitor\t\n+68\tprogenitor\t\n+69\tprogenitor\t\n+70\tprogenitor\t\n+71\tprogenitor\t\n+72\tprogenitor\t\n+73\tprogenitor\t\n+74\tprogenitor\t\n+75\tprogenitor\t\n+76\tprogenitor\t\n+77\tprogenitor\t\n+78\tprogenitor\t\n+79\tprogenitor\t\n+80\tMo\t\n+81\tMo\t\n+82\tMo\t\n+83\tMo\t\n+84\tMo\t\n+85\tMo\t\n+86\tMo\t\n+87\tMo\t\n+88\tMo\t\n+89\tMo\t\n+90\tMo\t\n+91\tMo\t\n+92\tMo\t\n+93\tMo\t\n+94\tMo\t\n+95\tMo\t\n+96\tMo\t\n+97\tMo\t\n+98\tMo\t\n+99\tMo\t\n+100\tMo\t\n+101\tMo\t\n+102\tMo\t\n+103\tMo\t\n+104\tMo\t\n+105\tMo\t\n+106\tMo\t\n+107\tMo\t\n+108\tMo\t\n+109\tMo\t\n+110\tMo\t\n+111\tMo\t\n+112\tMo\t\n+113\tMo\t\n+114\tMo\t\n+115\tMo\t\n+116\tMo\t\n+117\tMo\t\n+118\tMo\t\n+119\tMo\t\n+120\tMo\t\n+121\tMo\t\n+122\tMo\t\n+123\tMo\t\n+124\tMo\t\n+125\tMo\t\n+126\tMo\t\n+127\tMo\t\n+128\tMo\t\n+129\tMo\t\n+130\tMo\t\n+131\tMo\t\n+132\tMo\t\n+133\tMo\t\n+134\tMo\t\n+135\tMo\t\n+136\tMo\t\n+137\tMo\t\n+138\tMo\t\n+139\tMo\t\n+140\tMo\t\n+141\tMo\t\n+142\tMo\t\n+143\tMo\t\n+144\tMo\t\n+145\tMo\t\n+146\tMo\t\n+147\tMo\t\n+148\tMo\t\n+149\tMo\t\n+150\tMo\t\n+151\tMo\t\n+152\tMo\t\n+153\tMo\t\n+154\tMo\t\n+155\tMo\t\n+156\tMo\t\n+157\tMo\t\n+158\tMo\t\n+159\tMo\t\n+0\tprogenitor\t\n+1\tprogenitor\t\n+2\tprogenitor\t\n+3\tprogenitor\t\n+4\tprogenitor\t\n+5\tprogenitor\t\n+6\tprogenitor\t\n+7\tprogenitor\t\n+8\tprogenitor\t\n+9\tprogenitor\t\n+10\tprogenitor\t\n+11\tprogenitor\t\n+12\tprogenitor\t\n+13\tprogenitor\t\n+14\tprogenitor\t\n+15\tprogenitor\t\n+16\tprogenitor\t\n+17\tprogenitor\t\n+18\tprogenitor\t\n+19\tprogenitor\t\n+20\tprogenitor\t\n+21\tprogenitor\t\n+22\tprogenitor\t\n+23\tprogenitor\t\n+24\tprogenitor\t\n+25\tprogenitor\t\n+26\tprogenitor\t\n+27\tprogenitor\t\n+28\tprogenitor\t\n+29\tprogenitor\t\n+30\tprogenitor\t\n+31\tprogenitor\t\n+32\tprogenitor\t\n+33\tprogenitor\t\n+34\tprogenitor\t\n+35\tprogenitor\t\n+36\tprogenitor\t\n+37\tprogenitor\t\n+38\tprogenitor\t\n+39\tprogenitor\t\n+40\tprogenitor\t\n+41\tprogenitor\t\n+42\tprogenitor\t\n+43\tprogenitor\t\n+44\tprogenitor\t\n+45\tprogenitor\t\n+46\tprogenitor\t\n+47\tprogenitor\t\n+48\tprogenitor\t\n+49\tprogenitor\t\n+50\tprogenitor\t\n+51\tprogenitor\t\n+52\tprogenitor\t\n+53\tprogenitor\t\n+54\tprogenitor\t\n+55\tprogenitor\t\n+56\tprogenitor\t\n+57\tprogenitor\t\n+58\tprogenitor\t\n+59\tprogenitor\t\n+60\tprogenitor\t\n+61\tprogenitor\t\n+62\tprogenitor\t\n+63\tprogenitor\t\n+64\tprogenitor\t\n+65\tprogenitor\t\n+66\tprogenitor\t\n+67\tprogenitor\t\n+68\tprogenitor\t\n+69\tprogenitor\t\n+70\tprogenitor\t\n+71\tprogenitor\t\n+72\tprogenitor\t\n+73\tprogenitor\t\n+74\tprogenitor\t\n+75\tprogenitor\t\n+76\tprogenitor\t\n+77\tprogenitor\t\n+78\tprogenitor\t\n+79\tprogenitor\t\n+80\tEry\t\n+81\tEry\t\n+82\tEry\t\n+83\tEry\t\n+84\tEry\t\n+85\tEry\t\n+86\tEry\t\n+87\tEry\t\n+88\tEry\t\n+89\tEry\t\n+90\tEry\t\n+91\tEry\t\n+92\tEry\t\n+93\tEry\t\n+94\tEry\t\n+95\tEry\t\n+96\tEry\t\n+97\tEry\t\n+98\tEry\t\n+99\tEry\t\n+100\tEry\t\n+101\tEry\t\n+102\tEry\t\n+103\tEry\t\n+104\tEry\t\n+105\tEry\t\n+106\tEry\t\n+107\tEry\t\n+108\tEry\t\n+109\tEry\t\n+110\tEry\t\n+111\tEry\t\n+112\tEry\t\n+113\tEry\t\n+114\tEry\t\n+115\tEry\t\n+116\tEry\t\n+117\tEry\t\n+118\tEry\t\n+119\tEry\t\n+120\tEry\t\n+121\tEry\t\n+122\tEry\t\n+123\tEry\t\n+124\tEry\t\n+125\tEry\t\n+126\tEry\t\n+127\tEry\t\n+128\tEry\t\n+129\tEry\t\n+130\tEry\t\n+131\tEry\t\n+132\tEry\t\n+133\tEry\t\n+134\tEry\t\n+135\tEry\t\n+136\tEry\t\n+137\tEry\t\n+138\tEry\t\n+139\tEry\t\n+140\tEry\t\n+141\tEry\t\n+142\tEry\t\n+143\tEry\t\n+144\tEry\t\n+145\tEry\t\n+146\tEry\t\n+147\tEry\t\n+148\tEry\t\n+149\tEry\t\n+150\tEry\t\n+151\tEry\t\n+152\tEry\t\n+153\tEry'..b'genitor\t\n+2\tprogenitor\t\n+3\tprogenitor\t\n+4\tprogenitor\t\n+5\tprogenitor\t\n+6\tprogenitor\t\n+7\tprogenitor\t\n+8\tprogenitor\t\n+9\tprogenitor\t\n+10\tprogenitor\t\n+11\tprogenitor\t\n+12\tprogenitor\t\n+13\tprogenitor\t\n+14\tprogenitor\t\n+15\tprogenitor\t\n+16\tprogenitor\t\n+17\tprogenitor\t\n+18\tprogenitor\t\n+19\tprogenitor\t\n+20\tprogenitor\t\n+21\tprogenitor\t\n+22\tprogenitor\t\n+23\tprogenitor\t\n+24\tprogenitor\t\n+25\tprogenitor\t\n+26\tprogenitor\t\n+27\tprogenitor\t\n+28\tprogenitor\t\n+29\tprogenitor\t\n+30\tprogenitor\t\n+31\tprogenitor\t\n+32\tprogenitor\t\n+33\tprogenitor\t\n+34\tprogenitor\t\n+35\tprogenitor\t\n+36\tprogenitor\t\n+37\tprogenitor\t\n+38\tprogenitor\t\n+39\tprogenitor\t\n+40\tprogenitor\t\n+41\tprogenitor\t\n+42\tprogenitor\t\n+43\tprogenitor\t\n+44\tprogenitor\t\n+45\tprogenitor\t\n+46\tprogenitor\t\n+47\tprogenitor\t\n+48\tprogenitor\t\n+49\tprogenitor\t\n+50\tprogenitor\t\n+51\tprogenitor\t\n+52\tprogenitor\t\n+53\tprogenitor\t\n+54\tprogenitor\t\n+55\tprogenitor\t\n+56\tprogenitor\t\n+57\tprogenitor\t\n+58\tprogenitor\t\n+59\tprogenitor\t\n+60\tprogenitor\t\n+61\tprogenitor\t\n+62\tprogenitor\t\n+63\tprogenitor\t\n+64\tprogenitor\t\n+65\tprogenitor\t\n+66\tprogenitor\t\n+67\tprogenitor\t\n+68\tprogenitor\t\n+69\tprogenitor\t\n+70\tprogenitor\t\n+71\tprogenitor\t\n+72\tprogenitor\t\n+73\tprogenitor\t\n+74\tprogenitor\t\n+75\tprogenitor\t\n+76\tprogenitor\t\n+77\tprogenitor\t\n+78\tprogenitor\t\n+79\tprogenitor\t\n+80\tMk\t\n+81\tMk\t\n+82\tMk\t\n+83\tMk\t\n+84\tMk\t\n+85\tMk\t\n+86\tMk\t\n+87\tMk\t\n+88\tMk\t\n+89\tMk\t\n+90\tMk\t\n+91\tMk\t\n+92\tMk\t\n+93\tMk\t\n+94\tMk\t\n+95\tMk\t\n+96\tMk\t\n+97\tMk\t\n+98\tMk\t\n+99\tMk\t\n+100\tMk\t\n+101\tMk\t\n+102\tMk\t\n+103\tMk\t\n+104\tMk\t\n+105\tMk\t\n+106\tMk\t\n+107\tMk\t\n+108\tMk\t\n+109\tMk\t\n+110\tMk\t\n+111\tMk\t\n+112\tMk\t\n+113\tMk\t\n+114\tMk\t\n+115\tMk\t\n+116\tMk\t\n+117\tMk\t\n+118\tMk\t\n+119\tMk\t\n+120\tMk\t\n+121\tMk\t\n+122\tMk\t\n+123\tMk\t\n+124\tMk\t\n+125\tMk\t\n+126\tMk\t\n+127\tMk\t\n+128\tMk\t\n+129\tMk\t\n+130\tMk\t\n+131\tMk\t\n+132\tMk\t\n+133\tMk\t\n+134\tMk\t\n+135\tMk\t\n+136\tMk\t\n+137\tMk\t\n+138\tMk\t\n+139\tMk\t\n+140\tMk\t\n+141\tMk\t\n+142\tMk\t\n+143\tMk\t\n+144\tMk\t\n+145\tMk\t\n+146\tMk\t\n+147\tMk\t\n+148\tMk\t\n+149\tMk\t\n+150\tMk\t\n+151\tMk\t\n+152\tMk\t\n+153\tMk\t\n+154\tMk\t\n+155\tMk\t\n+156\tMk\t\n+157\tMk\t\n+158\tMk\t\n+159\tMk\t\n+0\tprogenitor\t\n+1\tprogenitor\t\n+2\tprogenitor\t\n+3\tprogenitor\t\n+4\tprogenitor\t\n+5\tprogenitor\t\n+6\tprogenitor\t\n+7\tprogenitor\t\n+8\tprogenitor\t\n+9\tprogenitor\t\n+10\tprogenitor\t\n+11\tprogenitor\t\n+12\tprogenitor\t\n+13\tprogenitor\t\n+14\tprogenitor\t\n+15\tprogenitor\t\n+16\tprogenitor\t\n+17\tprogenitor\t\n+18\tprogenitor\t\n+19\tprogenitor\t\n+20\tprogenitor\t\n+21\tprogenitor\t\n+22\tprogenitor\t\n+23\tprogenitor\t\n+24\tprogenitor\t\n+25\tprogenitor\t\n+26\tprogenitor\t\n+27\tprogenitor\t\n+28\tprogenitor\t\n+29\tprogenitor\t\n+30\tprogenitor\t\n+31\tprogenitor\t\n+32\tprogenitor\t\n+33\tprogenitor\t\n+34\tprogenitor\t\n+35\tprogenitor\t\n+36\tprogenitor\t\n+37\tprogenitor\t\n+38\tprogenitor\t\n+39\tprogenitor\t\n+40\tprogenitor\t\n+41\tprogenitor\t\n+42\tprogenitor\t\n+43\tprogenitor\t\n+44\tprogenitor\t\n+45\tprogenitor\t\n+46\tprogenitor\t\n+47\tprogenitor\t\n+48\tprogenitor\t\n+49\tprogenitor\t\n+50\tprogenitor\t\n+51\tprogenitor\t\n+52\tprogenitor\t\n+53\tprogenitor\t\n+54\tprogenitor\t\n+55\tprogenitor\t\n+56\tprogenitor\t\n+57\tprogenitor\t\n+58\tprogenitor\t\n+59\tprogenitor\t\n+60\tprogenitor\t\n+61\tprogenitor\t\n+62\tprogenitor\t\n+63\tprogenitor\t\n+64\tprogenitor\t\n+65\tprogenitor\t\n+66\tprogenitor\t\n+67\tprogenitor\t\n+68\tprogenitor\t\n+69\tprogenitor\t\n+70\tprogenitor\t\n+71\tprogenitor\t\n+72\tprogenitor\t\n+73\tprogenitor\t\n+74\tprogenitor\t\n+75\tprogenitor\t\n+76\tprogenitor\t\n+77\tprogenitor\t\n+78\tprogenitor\t\n+79\tprogenitor\t\n+80\tNeu\t\n+81\tNeu\t\n+82\tNeu\t\n+83\tNeu\t\n+84\tNeu\t\n+85\tNeu\t\n+86\tNeu\t\n+87\tNeu\t\n+88\tNeu\t\n+89\tNeu\t\n+90\tNeu\t\n+91\tNeu\t\n+92\tNeu\t\n+93\tNeu\t\n+94\tNeu\t\n+95\tNeu\t\n+96\tNeu\t\n+97\tNeu\t\n+98\tNeu\t\n+99\tNeu\t\n+100\tNeu\t\n+101\tNeu\t\n+102\tNeu\t\n+103\tNeu\t\n+104\tNeu\t\n+105\tNeu\t\n+106\tNeu\t\n+107\tNeu\t\n+108\tNeu\t\n+109\tNeu\t\n+110\tNeu\t\n+111\tNeu\t\n+112\tNeu\t\n+113\tNeu\t\n+114\tNeu\t\n+115\tNeu\t\n+116\tNeu\t\n+117\tNeu\t\n+118\tNeu\t\n+119\tNeu\t\n+120\tNeu\t\n+121\tNeu\t\n+122\tNeu\t\n+123\tNeu\t\n+124\tNeu\t\n+125\tNeu\t\n+126\tNeu\t\n+127\tNeu\t\n+128\tNeu\t\n+129\tNeu\t\n+130\tNeu\t\n+131\tNeu\t\n+132\tNeu\t\n+133\tNeu\t\n+134\tNeu\t\n+135\tNeu\t\n+136\tNeu\t\n+137\tNeu\t\n+138\tNeu\t\n+139\tNeu\t\n+140\tNeu\t\n+141\tNeu\t\n+142\tNeu\t\n+143\tNeu\t\n+144\tNeu\t\n+145\tNeu\t\n+146\tNeu\t\n+147\tNeu\t\n+148\tNeu\t\n+149\tNeu\t\n+150\tNeu\t\n+151\tNeu\t\n+152\tNeu\t\n+153\tNeu\t\n+154\tNeu\t\n+155\tNeu\t\n+156\tNeu\t\n+157\tNeu\t\n+158\tNeu\t\n+159\tNeu\t\n' |
| b |
| diff -r 000000000000 -r 6ea5a05a260a test-data/tl.score_genes_cell_cycle.krumsiek11.h5ad |
| b |
| Binary file test-data/tl.score_genes_cell_cycle.krumsiek11.h5ad has changed |
| b |
| diff -r 000000000000 -r 6ea5a05a260a test-data/tl.score_genes_cell_cycle.krumsiek11.obs.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/tl.score_genes_cell_cycle.krumsiek11.obs.tabular Mon Mar 04 10:15:02 2019 -0500 |
| b |
| b'@@ -0,0 +1,641 @@\n+index\tcell_type\tS_score\tG2M_score\tphase\n+0\tprogenitor\t0.2681\t0.20055\tS\n+1\tprogenitor\t0.24346666\t0.15855001\tS\n+2\tprogenitor\t0.2276\t0.13482499\tS\n+3\tprogenitor\t0.21043333\t0.12637499\tS\n+4\tprogenitor\t0.19113334\t0.1272\tS\n+5\tprogenitor\t0.17531666\t0.13072497\tS\n+6\tprogenitor\t0.16073334\t0.13242501\tS\n+7\tprogenitor\t0.15353334\t0.13672501\tS\n+8\tprogenitor\t0.14314999\t0.1399\tS\n+9\tprogenitor\t0.1337\t0.14515\tG2M\n+10\tprogenitor\t0.12695001\t0.15165001\tG2M\n+11\tprogenitor\t0.11726667\t0.16077498\tG2M\n+12\tprogenitor\t0.11081667\t0.16735\tG2M\n+13\tprogenitor\t0.104849994\t0.17429999\tG2M\n+14\tprogenitor\t0.09816667\t0.18152499\tG2M\n+15\tprogenitor\t0.095350005\t0.186625\tG2M\n+16\tprogenitor\t0.09528333\t0.19447501\tG2M\n+17\tprogenitor\t0.09463333\t0.199675\tG2M\n+18\tprogenitor\t0.0947\t0.205275\tG2M\n+19\tprogenitor\t0.0947\t0.20802501\tG2M\n+20\tprogenitor\t0.097733326\t0.21100001\tG2M\n+21\tprogenitor\t0.09881667\t0.21964999\tG2M\n+22\tprogenitor\t0.10131666\t0.22662501\tG2M\n+23\tprogenitor\t0.104849994\t0.23022501\tG2M\n+24\tprogenitor\t0.112266675\t0.23387499\tG2M\n+25\tprogenitor\t0.120283335\t0.2393\tG2M\n+26\tprogenitor\t0.12826668\t0.24174997\tG2M\n+27\tprogenitor\t0.13323334\t0.24710001\tG2M\n+28\tprogenitor\t0.13971666\t0.25280002\tG2M\n+29\tprogenitor\t0.14393334\t0.256775\tG2M\n+30\tprogenitor\t0.15066667\t0.259775\tG2M\n+31\tprogenitor\t0.15316668\t0.26244998\tG2M\n+32\tprogenitor\t0.15993333\t0.26487502\tG2M\n+33\tprogenitor\t0.16430001\t0.266275\tG2M\n+34\tprogenitor\t0.16598332\t0.270625\tG2M\n+35\tprogenitor\t0.17068332\t0.2715\tG2M\n+36\tprogenitor\t0.17713334\t0.276475\tG2M\n+37\tprogenitor\t0.17893334\t0.27514997\tG2M\n+38\tprogenitor\t0.18013333\t0.278025\tG2M\n+39\tprogenitor\t0.18251666\t0.279675\tG2M\n+40\tprogenitor\t0.18876666\t0.27925\tG2M\n+41\tprogenitor\t0.19041668\t0.281775\tG2M\n+42\tprogenitor\t0.19083333\t0.2824\tG2M\n+43\tprogenitor\t0.19411668\t0.281725\tG2M\n+44\tprogenitor\t0.19639999\t0.2844\tG2M\n+45\tprogenitor\t0.19843334\t0.285375\tG2M\n+46\tprogenitor\t0.20406666\t0.284075\tG2M\n+47\tprogenitor\t0.20673332\t0.28625\tG2M\n+48\tprogenitor\t0.20769998\t0.2885\tG2M\n+49\tprogenitor\t0.21186668\t0.28935\tG2M\n+50\tprogenitor\t0.21285\t0.28867498\tG2M\n+51\tprogenitor\t0.21443334\t0.28855002\tG2M\n+52\tprogenitor\t0.21568334\t0.28705\tG2M\n+53\tprogenitor\t0.21788335\t0.29035\tG2M\n+54\tprogenitor\t0.22551665\t0.28815\tG2M\n+55\tprogenitor\t0.22586668\t0.28689998\tG2M\n+56\tprogenitor\t0.23069999\t0.2816\tG2M\n+57\tprogenitor\t0.23118332\t0.282375\tG2M\n+58\tprogenitor\t0.23160002\t0.28230003\tG2M\n+59\tprogenitor\t0.23546667\t0.28329998\tG2M\n+60\tprogenitor\t0.23661667\t0.28195\tG2M\n+61\tprogenitor\t0.24134998\t0.27899998\tG2M\n+62\tprogenitor\t0.24546666\t0.27855\tG2M\n+63\tprogenitor\t0.24836665\t0.27609998\tG2M\n+64\tprogenitor\t0.25375\t0.27562502\tG2M\n+65\tprogenitor\t0.25834998\t0.273525\tG2M\n+66\tprogenitor\t0.26393333\t0.27015\tG2M\n+67\tprogenitor\t0.26746666\t0.26622498\tS\n+68\tprogenitor\t0.2706333\t0.267025\tS\n+69\tprogenitor\t0.27618334\t0.2651\tS\n+70\tprogenitor\t0.28033334\t0.263975\tS\n+71\tprogenitor\t0.2868167\t0.2622\tS\n+72\tprogenitor\t0.29141667\t0.26174998\tS\n+73\tprogenitor\t0.29198334\t0.26385\tS\n+74\tprogenitor\t0.29348332\t0.26275003\tS\n+75\tprogenitor\t0.29788333\t0.263575\tS\n+76\tprogenitor\t0.30125\t0.26232502\tS\n+77\tprogenitor\t0.29955\t0.261825\tS\n+78\tprogenitor\t0.30065\t0.2623\tS\n+79\tprogenitor\t0.30573332\t0.2588\tS\n+80\tMo\t0.30818334\t0.25555003\tS\n+81\tMo\t0.31073332\t0.25422502\tS\n+82\tMo\t0.31378332\t0.25410002\tS\n+83\tMo\t0.31268334\t0.25304997\tS\n+84\tMo\t0.31355\t0.25059998\tS\n+85\tMo\t0.3157\t0.251275\tS\n+86\tMo\t0.3139333\t0.25072497\tS\n+87\tMo\t0.3151833\t0.25165\tS\n+88\tMo\t0.3149333\t0.25079998\tS\n+89\tMo\t0.31440002\t0.25172502\tS\n+90\tMo\t0.31251666\t0.254725\tS\n+91\tMo\t0.31613332\t0.25347498\tS\n+92\tMo\t0.31813332\t0.25372502\tS\n+93\tMo\t0.31543335\t0.25340003\tS\n+94\tMo\t0.31663334\t0.257025\tS\n+95\tMo\t0.31793332\t0.25435\tS\n+96\tMo\t0.3184333\t0.2527\tS\n+97\tMo\t0.31743336\t0.25052497\tS\n+98\tMo\t0.3164667\t0.24747501\tS\n+99\tMo\t0.31841668\t0.2466\tS\n+100\tMo\t0.31648335\t0.24679999\tS\n+101\tMo\t0.31504998\t0.2501\tS\n+102\tMo\t0.31489998\t0.250375\tS\n+103\tMo\t0.31256667\t0.25195\tS\n+104\tMo\t0.31425\t0.250675\tS\n+105\tMo\t0.31441668\t0.248675\tS\n+106\tMo\t0.31828332\t0.24724999\tS\n+107\tMo\t0.32236665\t0.25105\tS\n+108\tMo\t0.32341668\t0.2527\tS\n+109\tMo\t0.32334998\t'..b'25013\tG2M\n+51\tprogenitor\t9.999983e-05\t-0.0017999709\tS\n+52\tprogenitor\t0.0018333336\t-0.01987499\tS\n+53\tprogenitor\t0.00090000033\t-0.032900006\tS\n+54\tprogenitor\t0.0029999996\t-0.05064997\tS\n+55\tprogenitor\t0.003983334\t-0.068574995\tS\n+56\tprogenitor\t-0.0008500004\t-0.08140004\tG1\n+57\tprogenitor\t-0.0029833335\t-0.09470001\tG1\n+58\tprogenitor\t-0.0021333336\t-0.106824994\tG1\n+59\tprogenitor\t-0.0015000002\t-0.11555001\tG1\n+60\tprogenitor\t-0.0022999998\t-0.12255001\tG1\n+61\tprogenitor\t-0.0017666668\t-0.13125\tG1\n+62\tprogenitor\t0.0033999998\t-0.14297503\tS\n+63\tprogenitor\t0.006316666\t-0.15117502\tS\n+64\tprogenitor\t0.005033333\t-0.15187496\tS\n+65\tprogenitor\t0.0031333338\t-0.15367502\tS\n+66\tprogenitor\t0.0035666667\t-0.15197498\tS\n+67\tprogenitor\t0.005016666\t-0.14580002\tS\n+68\tprogenitor\t0.0061\t-0.142575\tS\n+69\tprogenitor\t0.00515\t-0.13665\tS\n+70\tprogenitor\t0.0028499998\t-0.12865001\tS\n+71\tprogenitor\t0.0030833331\t-0.12112501\tS\n+72\tprogenitor\t0.0032833333\t-0.11669999\tS\n+73\tprogenitor\t0.0006166666\t-0.11475003\tS\n+74\tprogenitor\t-0.0006833335\t-0.11412498\tG1\n+75\tprogenitor\t-2.3283064e-10\t-0.11702502\tG1\n+76\tprogenitor\t0.0007333332\t-0.121425\tS\n+77\tprogenitor\t0.0005833333\t-0.12972501\tS\n+78\tprogenitor\t-0.0015333334\t-0.13869998\tG1\n+79\tprogenitor\t-0.0023\t-0.14877501\tG1\n+80\tNeu\t-0.0046166666\t-0.157125\tG1\n+81\tNeu\t-0.0035666665\t-0.16639996\tG1\n+82\tNeu\t-0.0011666667\t-0.17409998\tG1\n+83\tNeu\t-0.0026166667\t-0.180325\tG1\n+84\tNeu\t-0.0001833333\t-0.18502498\tG1\n+85\tNeu\t0.0035666665\t-0.18762502\tS\n+86\tNeu\t0.0024333335\t-0.19062501\tS\n+87\tNeu\t0.0023\t-0.19277498\tS\n+88\tNeu\t0.0014833333\t-0.19762498\tS\n+89\tNeu\t0.0024333335\t-0.201725\tS\n+90\tNeu\t0.003866667\t-0.20430002\tS\n+91\tNeu\t0.0067999996\t-0.20865002\tS\n+92\tNeu\t0.0079333335\t-0.21332502\tS\n+93\tNeu\t0.0068\t-0.21907501\tS\n+94\tNeu\t0.0058\t-0.22292498\tS\n+95\tNeu\t0.0069666663\t-0.22795\tS\n+96\tNeu\t0.0023833334\t-0.22915001\tS\n+97\tNeu\t0.0056166667\t-0.230375\tS\n+98\tNeu\t0.0051666666\t-0.23027502\tS\n+99\tNeu\t0.001966667\t-0.23169999\tS\n+100\tNeu\t0.0033666668\t-0.23169999\tS\n+101\tNeu\t0.0047333334\t-0.233675\tS\n+102\tNeu\t0.0045666667\t-0.23272496\tS\n+103\tNeu\t0.00060000026\t-0.23024999\tS\n+104\tNeu\t0.0036833333\t-0.22662503\tS\n+105\tNeu\t0.0025166667\t-0.22107498\tS\n+106\tNeu\t0.0038833334\t-0.22109997\tS\n+107\tNeu\t0.0033666666\t-0.21907501\tS\n+108\tNeu\t0.0042666667\t-0.218675\tS\n+109\tNeu\t0.0038\t-0.2165\tS\n+110\tNeu\t0.004633333\t-0.21385\tS\n+111\tNeu\t0.003266667\t-0.21305001\tS\n+112\tNeu\t0.0034166668\t-0.21077499\tS\n+113\tNeu\t0.0017166669\t-0.21184999\tS\n+114\tNeu\t0.0012666667\t-0.21437502\tS\n+115\tNeu\t-0.0016333334\t-0.2153\tG1\n+116\tNeu\t-0.00043333336\t-0.215675\tG1\n+117\tNeu\t0.0018833333\t-0.21865001\tS\n+118\tNeu\t0.0014666667\t-0.22187501\tS\n+119\tNeu\t-0.0020833332\t-0.21787499\tG1\n+120\tNeu\t-0.0039000001\t-0.21329997\tG1\n+121\tNeu\t-0.0023\t-0.20820004\tG1\n+122\tNeu\t-0.00195\t-0.21035\tG1\n+123\tNeu\t-0.0058833333\t-0.20732501\tG1\n+124\tNeu\t-0.0070166667\t-0.20714998\tG1\n+125\tNeu\t-0.008633333\t-0.20389998\tG1\n+126\tNeu\t-0.006616667\t-0.20832503\tG1\n+127\tNeu\t-0.003116667\t-0.21047503\tG1\n+128\tNeu\t-0.0055833333\t-0.21289998\tG1\n+129\tNeu\t-0.0042333333\t-0.216575\tG1\n+130\tNeu\t-0.005016667\t-0.21945003\tG1\n+131\tNeu\t-0.0020833334\t-0.21799998\tG1\n+132\tNeu\t-0.0032\t-0.21150002\tG1\n+133\tNeu\t-0.0033333339\t-0.20989999\tG1\n+134\tNeu\t-0.0011666667\t-0.21257499\tG1\n+135\tNeu\t-0.0023\t-0.21222499\tG1\n+136\tNeu\t-0.0034666667\t-0.2146\tG1\n+137\tNeu\t-0.0011833335\t-0.21350002\tG1\n+138\tNeu\t-0.00325\t-0.21377501\tG1\n+139\tNeu\t-0.0040166667\t-0.213925\tG1\n+140\tNeu\t-0.0024666665\t-0.21455\tG1\n+141\tNeu\t0.0028333336\t-0.21975\tS\n+142\tNeu\t0.0032833333\t-0.220325\tS\n+143\tNeu\t0.004766667\t-0.22119999\tS\n+144\tNeu\t0.00705\t-0.22362499\tS\n+145\tNeu\t0.0036\t-0.22555003\tS\n+146\tNeu\t0.006733333\t-0.22377498\tS\n+147\tNeu\t0.0025000002\t-0.22509998\tS\n+148\tNeu\t0.0018\t-0.221075\tS\n+149\tNeu\t6.666663e-05\t-0.22125\tS\n+150\tNeu\t-0.0014499999\t-0.219875\tG1\n+151\tNeu\t-0.0012833332\t-0.21900001\tG1\n+152\tNeu\t-0.0001999999\t-0.21767499\tG1\n+153\tNeu\t-0.0032666668\t-0.21407498\tG1\n+154\tNeu\t-0.0017\t-0.2116\tG1\n+155\tNeu\t-0.0028166666\t-0.2077\tG1\n+156\tNeu\t-0.00245\t-0.2053\tG1\n+157\tNeu\t-0.0011166666\t-0.203825\tG1\n+158\tNeu\t-0.001966667\t-0.20535001\tG1\n+159\tNeu\t-0.0027\t-0.20725003\tG1\n' |
| b |
| diff -r 000000000000 -r 6ea5a05a260a test-data/tl.tsne.krumsiek11.h5ad |
| b |
| Binary file test-data/tl.tsne.krumsiek11.h5ad has changed |
| b |
| diff -r 000000000000 -r 6ea5a05a260a test-data/tl.tsne.krumsiek11_X_tsne.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/tl.tsne.krumsiek11_X_tsne.tabular Mon Mar 04 10:15:02 2019 -0500 |
| b |
| b'@@ -0,0 +1,640 @@\n+1.519449996948242188e+01\t-1.959712028503417969e+01\n+1.430198860168457031e+01\t-1.977149772644042969e+01\n+1.366461181640625000e+01\t-1.944742584228515625e+01\n+1.320474624633789062e+01\t-1.861057281494140625e+01\n+1.247396755218505859e+01\t-1.828991889953613281e+01\n+1.173612689971923828e+01\t-1.787339973449707031e+01\n+1.088126182556152344e+01\t-1.741477966308593750e+01\n+1.004744911193847656e+01\t-1.688929176330566406e+01\n+9.242062568664550781e+00\t-1.633218383789062500e+01\n+8.551974296569824219e+00\t-1.572820758819580078e+01\n+7.994421005249023438e+00\t-1.496002674102783203e+01\n+7.534011363983154297e+00\t-1.414666461944580078e+01\n+7.137795925140380859e+00\t-1.332961750030517578e+01\n+6.881215572357177734e+00\t-1.266186618804931641e+01\n+6.554283618927001953e+00\t-1.194301605224609375e+01\n+6.316970825195312500e+00\t-1.134942722320556641e+01\n+6.111618518829345703e+00\t-1.060422611236572266e+01\n+5.999991416931152344e+00\t-9.829056739807128906e+00\n+5.852959632873535156e+00\t-8.975935935974121094e+00\n+5.754123687744140625e+00\t-8.093419075012207031e+00\n+5.681646823883056641e+00\t-7.331385612487792969e+00\n+5.690028667449951172e+00\t-6.516033649444580078e+00\n+5.646613597869873047e+00\t-5.590456008911132812e+00\n+5.599578380584716797e+00\t-4.722455978393554688e+00\n+5.614356040954589844e+00\t-3.809689283370971680e+00\n+5.634355068206787109e+00\t-2.910351276397705078e+00\n+5.672942161560058594e+00\t-1.983908414840698242e+00\n+5.692958831787109375e+00\t-1.081819057464599609e+00\n+5.783164501190185547e+00\t-2.481995671987533569e-01\n+5.843826293945312500e+00\t7.042319178581237793e-01\n+5.949952125549316406e+00\t1.492690682411193848e+00\n+6.069711208343505859e+00\t2.275426864624023438e+00\n+6.275776386260986328e+00\t3.030730962753295898e+00\n+6.595882892608642578e+00\t3.702220201492309570e+00\n+7.062664508819580078e+00\t4.283195495605468750e+00\n+7.793676853179931641e+00\t4.937045097351074219e+00\n+8.450625419616699219e+00\t5.439468860626220703e+00\n+8.976801872253417969e+00\t5.800347328186035156e+00\n+9.408540725708007812e+00\t6.086088657379150391e+00\n+9.624043464660644531e+00\t6.300896167755126953e+00\n+9.998101234436035156e+00\t6.388058185577392578e+00\n+1.015411567687988281e+01\t6.684517383575439453e+00\n+1.054878711700439453e+01\t6.530696868896484375e+00\n+1.051755142211914062e+01\t7.047624111175537109e+00\n+1.096314525604248047e+01\t6.734574794769287109e+00\n+1.081092071533203125e+01\t7.304609775543212891e+00\n+1.132081222534179688e+01\t6.912662506103515625e+00\n+1.108376121520996094e+01\t7.558815956115722656e+00\n+1.164056396484375000e+01\t7.036955833435058594e+00\n+1.156700229644775391e+01\t7.518383026123046875e+00\n+1.154088020324707031e+01\t7.928282260894775391e+00\n+1.207668018341064453e+01\t7.159606933593750000e+00\n+1.173250007629394531e+01\t8.000703811645507812e+00\n+1.227454090118408203e+01\t7.442850112915039062e+00\n+1.242261028289794922e+01\t7.537978172302246094e+00\n+1.215592193603515625e+01\t8.201261520385742188e+00\n+1.233993148803710938e+01\t8.318535804748535156e+00\n+1.286047077178955078e+01\t7.827185630798339844e+00\n+1.295083713531494141e+01\t8.165453910827636719e+00\n+1.292353916168212891e+01\t8.663576126098632812e+00\n+1.346461200714111328e+01\t8.328847885131835938e+00\n+1.345806503295898438e+01\t8.873760223388671875e+00\n+1.391223335266113281e+01\t8.757353782653808594e+00\n+1.401749229431152344e+01\t9.183512687683105469e+00\n+1.442186355590820312e+01\t9.189196586608886719e+00\n+1.467169475555419922e+01\t9.464248657226562500e+00\n+1.498757743835449219e+01\t9.662472724914550781e+00\n+1.532551097869873047e+01\t9.858908653259277344e+00\n+1.565018653869628906e+01\t1.008980083465576172e+01\n+1.600958251953125000e+01\t1.033419132232666016e+01\n+1.638028717041015625e+01\t1.058873081207275391e+01\n+1.671751213073730469e+01\t1.081599426269531250e+01\n+1.702677536010742188e+01\t1.102662467956542969e+01\n+1.735839462280273438e+01\t1.126764965057373047e+01\n+1.768183517456054688e+01\t1.148044204711914062e+01\n+1.798530006408691406e+01\t1.169673252105712891e+01\n+1.830868339538574219e+01\t1.191948986053466797e+01\n+1.863975524902343750e+01'..b'.430453491210937500e+01\n+-1.040180301666259766e+01\t-3.444690704345703125e+01\n+-1.051032924652099609e+01\t-3.453202819824218750e+01\n+-1.091506290435791016e+01\t-3.476406860351562500e+01\n+-1.149002265930175781e+01\t-3.500469589233398438e+01\n+-1.197370433807373047e+01\t-3.517875289916992188e+01\n+-1.232476329803466797e+01\t-3.519157791137695312e+01\n+-1.294825935363769531e+01\t-3.516530990600585938e+01\n+-1.365509510040283203e+01\t-3.510067749023437500e+01\n+-1.494047737121582031e+01\t-3.510100555419921875e+01\n+-1.603278160095214844e+01\t-3.530395126342773438e+01\n+-1.675340843200683594e+01\t-3.538857650756835938e+01\n+-1.685874938964843750e+01\t-3.548091506958007812e+01\n+-1.720363044738769531e+01\t-3.578920364379882812e+01\n+-1.728767013549804688e+01\t-3.575481796264648438e+01\n+-1.765481567382812500e+01\t-3.578696060180664062e+01\n+-1.770997047424316406e+01\t-3.586181640625000000e+01\n+-1.802918624877929688e+01\t-3.607511138916015625e+01\n+-1.811597633361816406e+01\t-3.632243728637695312e+01\n+-1.818618965148925781e+01\t-3.667174530029296875e+01\n+-1.818774414062500000e+01\t-3.734482192993164062e+01\n+-1.822867012023925781e+01\t-3.886906051635742188e+01\n+-1.810912132263183594e+01\t-3.913828659057617188e+01\n+-1.797933578491210938e+01\t-3.962589645385742188e+01\n+-1.796797180175781250e+01\t-3.975232315063476562e+01\n+-1.775218009948730469e+01\t-4.022003555297851562e+01\n+-1.732578849792480469e+01\t-4.068730926513671875e+01\n+-1.690691375732421875e+01\t-4.064323806762695312e+01\n+-1.648787307739257812e+01\t-4.081156158447265625e+01\n+-1.638434219360351562e+01\t-4.061108398437500000e+01\n+-1.680851173400878906e+01\t-4.017563629150390625e+01\n+-1.704722785949707031e+01\t-3.969401168823242188e+01\n+-1.717719459533691406e+01\t-3.948302078247070312e+01\n+-1.720919418334960938e+01\t-3.910422134399414062e+01\n+-1.715806961059570312e+01\t-3.882429885864257812e+01\n+-1.673982048034667969e+01\t-3.908253097534179688e+01\n+-1.371504497528076172e+01\t-3.877840805053710938e+01\n+-1.305936717987060547e+01\t-3.902551651000976562e+01\n+-1.310692214965820312e+01\t-3.922296524047851562e+01\n+-1.254828739166259766e+01\t-3.958239746093750000e+01\n+-1.200624752044677734e+01\t-3.997818374633789062e+01\n+-1.164904689788818359e+01\t-3.977762603759765625e+01\n+-1.198938465118408203e+01\t-4.017607116699218750e+01\n+-1.291513729095458984e+01\t-4.103605651855468750e+01\n+-1.404931831359863281e+01\t-4.105354309082031250e+01\n+-1.425574493408203125e+01\t-4.136027145385742188e+01\n+-1.431068229675292969e+01\t-4.164620971679687500e+01\n+-1.393457221984863281e+01\t-4.161294937133789062e+01\n+-1.195437526702880859e+01\t-4.098776245117187500e+01\n+-1.204803180694580078e+01\t-4.089416503906250000e+01\n+-1.241441440582275391e+01\t-4.070640182495117188e+01\n+-1.255411720275878906e+01\t-4.045176315307617188e+01\n+-1.321313571929931641e+01\t-3.998711013793945312e+01\n+-1.294196605682373047e+01\t-4.011898803710937500e+01\n+-1.318817043304443359e+01\t-4.022884750366210938e+01\n+-1.352913379669189453e+01\t-4.006181716918945312e+01\n+-1.343410015106201172e+01\t-3.986800384521484375e+01\n+-1.463830280303955078e+01\t-3.964513778686523438e+01\n+-1.519129276275634766e+01\t-3.914448165893554688e+01\n+-1.532430076599121094e+01\t-3.890964889526367188e+01\n+-1.599927234649658203e+01\t-3.833520889282226562e+01\n+-1.656130027770996094e+01\t-3.767085647583007812e+01\n+-1.636859703063964844e+01\t-3.757136535644531250e+01\n+-1.660573577880859375e+01\t-3.731252288818359375e+01\n+-1.584738540649414062e+01\t-3.749007797241210938e+01\n+-1.584149074554443359e+01\t-3.753525161743164062e+01\n+-1.577875041961669922e+01\t-3.789312744140625000e+01\n+-1.547798728942871094e+01\t-3.753144836425781250e+01\n+-1.501726150512695312e+01\t-3.742636871337890625e+01\n+-1.278185081481933594e+01\t-3.781040191650390625e+01\n+-1.196537017822265625e+01\t-3.777410125732421875e+01\n+-1.159818267822265625e+01\t-3.774356079101562500e+01\n+-1.136351585388183594e+01\t-3.779747009277343750e+01\n+-1.120591926574707031e+01\t-3.794934082031250000e+01\n+-1.131576633453369141e+01\t-3.840375137329101562e+01\n+-1.147500324249267578e+01\t-3.856223678588867188e+01\n' |
| b |
| diff -r 000000000000 -r 6ea5a05a260a test-data/tl.umap.neighbors_umap_euclidean.recipe_weinreb17.paul15_subsample.h5ad |
| b |
| Binary file test-data/tl.umap.neighbors_umap_euclidean.recipe_weinreb17.paul15_subsample.h5ad has changed |
