| Previous changeset 0:5d2e17328afe (2019-03-04) Next changeset 2:7d22964a8639 (2019-12-05) |
|
Commit message:
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" |
|
modified:
README.md inspect.xml macros.xml test-data/pl.clustermap.krumsiek11.png test-data/pl.dotplot.krumsiek11.png test-data/pl.pca_overview.pp.pca.krumsiek11.png test-data/pl.scatter.krumsiek11.png test-data/pp.filter_cells.krumsiek11-min_counts.h5ad test-data/pp.filter_genes.krumsiek11-min_counts.h5ad test-data/pp.filter_genes_dispersion.krumsiek11-seurat.h5ad 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.pca.krumsiek11.h5ad test-data/pp.recipe_seurat.recipe_zheng17.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/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.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.rank_genes_groups.krumsiek11.h5ad test-data/tl.score_genes.krumsiek11.h5ad test-data/tl.score_genes_cell_cycle.krumsiek11.h5ad test-data/tl.tsne.krumsiek11.h5ad test-data/tl.umap.neighbors_umap_euclidean.recipe_weinreb17.paul15_subsample.h5ad |
|
added:
test-data/blobs.h5ad test-data/pl.draw_graph.png test-data/pl.highly_variable_genes.seurat.blobs.png test-data/pl.rank_genes_groups.rank_genes_groups.krumsiek11.png test-data/pl.rank_genes_groups_violin.Ery.png test-data/pl.rank_genes_groups_violin.Mk.png test-data/pl.rank_genes_groups_violin.Mo.png test-data/pl.rank_genes_groups_violin.Neu.png test-data/pl.rank_genes_groups_violin.progenitor.png test-data/pl.scatter.umap.pbmc68k_reduced.png test-data/pl.stacked_violin.krumsiek11.png test-data/pp.calculate_qc_metrics.sparce_csr_matrix.h5ad test-data/pp.combat.blobs.h5ad test-data/pp.downsample_counts.random-randint.h5ad test-data/pp.filter_cells.krumsiek11-max_genes.h5ad test-data/pp.filter_rank_genes_groups.h5ad test-data/pp.highly_variable_genes.krumsiek11-cell_ranger.h5ad test-data/pp.highly_variable_genes.seurat.blobs.h5ad test-data/pp.normalize_total.krumsiek11.h5ad test-data/pp.recipe_weinreb17.paul15_subsample.updated.h5ad test-data/sparce_csr_matrix.h5ad test-data/tl.draw_graph.pp.neighbors_umap_euclidean.recipe_weinreb17.paul15_subsample.h5ad test-data/tl.leiden.neighbors_gauss_braycurtis.recipe_weinreb17.paul15_subsample.h5ad test-data/tl.rank_genes_groups.liblinear.krumsiek11.h5ad test-data/tl.rank_genes_groups.newton-cg.pbmc68k_reduced.h5ad |
|
removed:
README.rst test-data/pp.filter_cells.number_per_cell.krumsiek11-max_genes.tabular 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.per_gene.krumsiek11-cell_ranger.tabular test-data/pp.filter_genes_dispersion.per_gene.krumsiek11-seurat.tabular test-data/pp.normalize_per_cell.obs.krumsiek11.tabular test-data/tl.diffmap.neighbors_gauss_braycurtis.recipe_weinreb17.paul15_subsample.X_diffmap.tabular test-data/tl.dpt.diffmap.neighbors_gauss_braycurtis.recipe_weinreb17.paul15_subsample.obs.tabular test-data/tl.score_genes.krumsiek11.obs.tabular test-data/tl.score_genes_cell_cycle.krumsiek11.obs.tabular |
| b |
| diff -r 5d2e17328afe -r a755eaa1cc32 README.md --- a/README.md Mon Mar 04 10:15:38 2019 -0500 +++ b/README.md Wed Oct 16 06:31:52 2019 -0400 |
| [ |
| b'@@ -1,138 +1,115 @@\n Scanpy\n ======\n \n-## Classification of methods into steps\n+1. Inspect & Manipulate (`inspect.xml`)\n \n-Steps:\n+ Methods | Description\n+ --- | ---\n+ `pp.calculate_qc_metrics` | Calculate quality control metrics\n+ `pp.neighbors` | Compute a neighborhood graph of observations\n+ `tl.score_genes` | Score a set of genes\n+ `tl.score_genes_cell_cycle` | Score cell cycle gene\n+ `tl.rank_genes_groups` | Rank genes for characterizing groups\n+ `tl.marker_gene_overlap` | Calculate an overlap score between data-deriven marker genes and provided markers (**not working for now**)\n+ `pp.log1p` | Logarithmize the data matrix.\n+ `pp.scale` | Scale data to unit variance and zero mean\n+ `pp.sqrt` | Square root the data matrix\n \n-1. Filtering\n+2. Filter (`filter.xml`)\n \n Methods | Description\n --- | ---\n `pp.filter_cells` | Filter cell outliers based on counts and numbers of genes expressed.\n `pp.filter_genes` | Filter genes based on number of cells or counts.\n- `pp.filter_genes_dispersion` | Extract highly variable genes\n+ `tl.filter_rank_genes_groups` | Filters out genes based on fold change and fraction of genes expressing the gene within and outside the groupby categories (**to fix**)\n `pp.highly_variable_genes` | Extract highly variable genes\n `pp.subsample` | Subsample to a fraction of the number of observations\n- `queries.gene_coordinates` | (Could not find...)\n- `queries.mitochondrial_genes` | Retrieves Mitochondrial gene symbols for specific organism through BioMart for filtering\n-\n-2. Quality Plots\n-\n- These are in-between stages used to measure the effectiveness of a Filtering/Normalisation/Conf.Removal stage either after processing or prior to.\n+ `pp.downsample_counts` | Downsample counts so that each cell has no more than target_counts\n \n- Methods | Description | Notes\n- --- | --- | ---\n- `pp.calculate_qc_metrics` | Calculate quality control metrics\n- `pl.violin` | violin plot of features, lib. size, or subsets of. \n- `pl.stacked_violin` | Same as above but for multiple series of features or cells\n-\n-3. Normalization\n+3. Normalize (`normalize.xml`)\n \n Methods | Description\n --- | ---\n- `pp.normalize_per_cell` | Normalize total counts per cell\n+ `pp.normalize_total` | Normalize counts per cell\n `pp.recipe_zheng17` | Normalization and filtering as of [Zheng17]\n `pp.recipe_weinreb17` | Normalization and filtering as of [Weinreb17]\n `pp.recipe_seurat` | Normalization and filtering as of Seurat [Satija15]\n- `pp.log1p` | Logarithmize the data matrix.\n- `pp.scale` | Scale data to unit variance and zero mean\n- `pp.sqrt` | \n- `pp.downsample_counts` | Downsample counts so that each cell has no more than target_counts\n \n-4. Conf. removal\n+4. Remove confounders (`remove_confounder.xml`)\n \n Methods | Description\n --- | ---\n `pp.regress_out` | Regress out unwanted sources of variation\n `pp.mnn_correct` | Correct batch effects by matching mutual nearest neighbors\n- `pp.dca` | Deep count autoencoder to denoise the data\n- `pp.magic` | Markov Affinity-based Graph Imputation of Cells (MAGIC) API to denoise\n- `tl.sim` | Simulate dynamic gene expression data [Wittman09]\n- `pp.calculate_qc_metrics` | Calculate quality control metrics\n- `tl.score_genes` | Score a set of genes\n- `tl.score_genes_cell_cycle` | Score cell cycle genes\n- `tl.cyclone` | Assigns scores and predicted class to observations based on cell-cycle genes [Scialdone15]\n- `tl.sandbag` | Calculates pairs of genes serving as markers for each cell-cycle phase [Scialdone15]\n+ `pp.combat` | ComBat function for batch effect correction\n \n-5. Clustering and Heatmaps\n+5. Clustering, embedding and trajectory inference (`cluster_reduce_dimension.xml`)\n \n Methods | Description\n --- | ---\n- `tl.leiden` | Cluster cells into subgroups [Traag18] [Levine15]\n- `tl.louvain` | Cluster cells into subgroups [Blondel08] [Lev'..b"| Heatmap of the expression values of set of genes\n+ `pl.dotplot` | Makes a dot plot of the expression values\n+ `pl.violin` | Violin plot\n+ `pl.stacked_violin` | Stacked violin plots\n+ `pl.matrixplot` | Heatmap of the mean expression values per cluster\n+ `pl.clustermap` | Hierarchically-clustered heatmap\n \n-6. Cluster Inspection and plotting\n+ 2. Preprocessing\n \n- Methods that draw out the clusters computed in the previous stage, not heatmap or pseudotime related.\n+ Methods | Description\n+ --- | ---\n+ `pl.highest_expr_genes` | Plot the fraction of counts assigned to each gene over all cells\n+ `pl.highly_variable_genes` | Plot dispersions versus means for genes\n+\n+ 3. PCA\n \n- Methods | Description \n- --- | --- \n- `pl.clustermap` |\n- `pl.phate` | \n- `pl.dotplot` | \n- `pl.draw_graph` | (really general purpose, would not implement directly)\n- `pl.filter_genes_dispersion` | (depreciated for 'highly_variable_genes')\n- `pl.matrix` | (could not find in API)\n- `pl.pca` | \n- `pl.pca_loadings` | \n- `pl.pca_overview` | \n- `pl.pca_variance_ratio` | \n- `pl.ranking` | (not sure what this does...)\n- `pl.scatter` | ([very general purpose](https://icb-scanpy.readthedocs-hosted.com/en/latest/api/scanpy.api.pl.scatter.html), would not implement directly)\n- `pl.set_rcParams_defaults` | \n- `pl.set_rcParams_scanpy` | \n- `pl.sim` | \n- `pl.tsne` | \n- `pl.umap` | \n+ Methods | Description\n+ --- | ---\n+ `pl.pca` | Scatter plot in PCA coordinates\n+ `pl.pca_loadings` | Rank genes according to contributions to PCs\n+ `pl.pca_variance_ratio` | Scatter plot in PCA coordinates\n+ `pl.pca_overview` | Plot PCA results\n \n-7. Branch/Between-Cluster Inspection\n+ 4. Embeddings\n \n- Pseudotime analysis, relies on initial clustering.\n+ Methods | Description\n+ --- | ---\n+ `pl.tsne` | Scatter plot in tSNE basis\n+ `pl.umap` | Scatter plot in UMAP basis\n+ `pl.diffmap` | Scatter plot in Diffusion Map basis\n+ `pl.draw_graph` | Scatter plot in graph-drawing basis\n \n- Methods | Description\n- --- | ---\n- `tl.dpt` | Infer progression of cells through geodesic distance along the graph [Haghverdi16] [Wolf17i]\n- `pl.dpt_groups_pseudotime` | \n- `pl.dpt_timeseries` | \n- `tl.paga_compare_paths` | \n- `tl.paga_degrees` | \n- `tl.paga_expression_entropies` | \n- `tl.paga` | Generate cellular maps of differentiation manifolds with complex topologies [Wolf17i]\n- `pl.paga` | \n- `pl.paga_adjacency` | \n- `pl.paga_compare` | \n- `pl.paga_path` | \n- `pl.timeseries` | \n- `pl.timeseries_as_heatmap` | \n- `pl.timeseries_subplot` | \n+ 5. Branching trajectories and pseudotime, clustering\n \n+ Methods | Description\n+ --- | ---\n+ `pl.dpt_groups_pseudotime` | Plot groups and pseudotime\n+ `pl.dpt_timeseries` | Heatmap of pseudotime series\n+ `pl.paga` | Plot the abstracted graph through thresholding low-connectivity edges\n+ `pl.paga_compare` | Scatter and PAGA graph side-by-side\n+ `pl.paga_path` | Gene expression and annotation changes along paths\n \n-Methods to sort | Description\n---- | --- \n-`tl.ROC_AUC_analysis` | (could not find in API)\n-`tl.correlation_matrix` | (could not find in API)\n-`rtools.mnn_concatenate` | (could not find in API)\n-`utils.compute_association_matrix_of_groups` | (could not find in API) \n-`utils.cross_entropy_neighbors_in_rep` | (could not find in API)\n-`utils.merge_groups` | (could not find in API)\n-`utils.plot_category_association` | (could not find in API)\n-`utils.select_groups` | (could not find in API)\n\\ No newline at end of file\n+ 6. Marker genes\n+\n+ Methods | Description\n+ --- | ---\n+ `pl.rank_genes_groups` | Plot ranking of genes using dotplot plot\n+ `pl.rank_genes_groups_violin` | Plot ranking of genes for all tested comparisons\n" |
| b |
| diff -r 5d2e17328afe -r a755eaa1cc32 README.rst --- a/README.rst Mon Mar 04 10:15:38 2019 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,105 +0,0 @@ -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 5d2e17328afe -r a755eaa1cc32 inspect.xml --- a/inspect.xml Mon Mar 04 10:15:38 2019 -0500 +++ b/inspect.xml Wed Oct 16 06:31:52 2019 -0400 |
| [ |
| b'@@ -1,7 +1,52 @@\n-<tool id="scanpy_inspect" name="Inspect with scanpy" version="@galaxy_version@">\n- <description></description>\n+<tool id="scanpy_inspect" name="Inspect and manipulate" version="@galaxy_version@">\n+ <description> with scanpy</description>\n <macros>\n <import>macros.xml</import>\n+ <xml name="score_genes_params">\n+ <param argument="n_bins" type="integer" value="25" label="Number of expression level bins for sampling" help=""/>\n+ <param argument="random_state" type="integer" value="0" label="Random seed for sampling" help=""/>\n+ <expand macro="param_use_raw"/>\n+ </xml>\n+ <token name="@CMD_score_genes_inputs@"><![CDATA[\n+ n_bins=$method.n_bins,\n+ random_state=$method.random_state,\n+ use_raw=$method.use_raw,\n+ copy=False\n+ ]]></token>\n+ <xml name="corr_method">\n+ <param argument="corr_method" type="select" label="P-value correction method">\n+ <option value="benjamini-hochberg">Benjamini-Hochberg</option>\n+ <option value="bonferroni">Bonferroni</option>\n+ </param>\n+ </xml>\n+ <xml name="fit_intercept">\n+ <param argument="fit_intercept" type="boolean" truevalue="True" falsevalue="False" checked="true"\n+ label="Should a constant (a.k.a. bias or intercept) be added to the decision function?" help=""/>\n+ </xml>\n+ <xml name="max_iter">\n+ <param argument="max_iter" type="integer" min="0" value="100" label="Maximum number of iterations taken for the solvers to converge" help=""/>\n+ </xml>\n+ <xml name="multi_class">\n+ <param argument="multi_class" type="select" label="Multi class" help="">\n+ <option value="ovr">ovr: a binary problem is fit for each label</option>\n+ <option value="multinomial">multinomial: the multinomial loss fit across the entire probability distribution, even when the data is binary</option>\n+ <option value="auto">auto: selects \xe2\x80\x98ovr\xe2\x80\x99 if the data is binary and otherwise selects \xe2\x80\x98multinomial\xe2\x80\x99</option>\n+ </param>\n+ </xml>\n+ <xml name="penalty">\n+ <param argument="penalty" type="select" label="Norm used in the penalization" help="">\n+ <option value="l1">l1</option>\n+ <option value="l2">l2</option>\n+ <option value="customized">customized</option>\n+ </param>\n+ </xml>\n+ <xml name="custom_penalty">\n+ <param argument="pen" type="text" value="" label="Norm used in the penalization" help=""/>\n+ </xml>\n+ <xml name="random_state">\n+ <param argument="random_state" type="integer" value="" optional="true"\n+ label="The seed of the pseudo random number generator to use when shuffling the data" help=""/>\n+ </xml>\n </macros>\n <expand macro="requirements"/>\n <expand macro="version_command"/>\n@@ -13,22 +58,195 @@\n @CMD_imports@\n @CMD_read_inputs@\n \n-#if $method.method == "tl.paga"\n-sc.tl.paga(\n+#if $method.method == "pp.calculate_qc_metrics"\n+sc.pp.calculate_qc_metrics(\n+ adata=adata,\n+ expr_type=\'$method.expr_type\',\n+ var_type=\'$method.var_type\',\n+ #if str($method.qc_vars) != \'\'\n+ #set $qc_vars = [str(x.strip()) for x in str($method.qc_vars).split(\',\')]\n+ qc_vars=$qc_vars,\n+ #end if\n+ #if str($method.percent_top) != \'\'\n+ #set $percent_top = [int(x.strip()) for x in str($method.percent_top).split(\',\')]\n+ percent_top=$method.percent_top,\n+ #end if\n+ inplace=True)\n+\n+#else if $method.method == "tl.score_genes"\n+sc.tl.score_genes(\n adata=adata,\n- groups=\'$method.groups\',\n- use_rna_velocity =$method.use_rna_velocity,\n- model=\'$method.model\',\n+ #set $gene_list = [str(x.strip()) for x in str($method.gene_list).split(\',\')]\n+ gene_list=$gene_list,\n+ ctrl_size=$method.ctrl_size,\n+ score_name=\'$method.scor'..b'tion.\n+Given two lists of genes associated to S phase and G2M phase, calculates\n+scores and assigns a cell cycle phase (G1, S or G2M). See\n+`score_genes` for more explanation.\n+\n+More details on the `scanpy documentation\n+<https://icb-scanpy.readthedocs-hosted.com/en/stable/api/scanpy.tl.score_genes_cell_cycle.html>`__\n+\n+Rank genes for characterizing groups, using `tl.rank_genes_groups`\n+==================================================================\n \n-More details on the `tl.paga scanpy documentation\n-<https://scanpy.readthedocs.io/en/latest/api/scanpy.api.tl.paga.html#scanpy.api.tl.paga>`_\n+The returned AnnData object contains:\n+\n+- Gene names, ordered according to scores\n+- Z-score underlying the computation of a p-value for each gene for each group, prdered according to scores\n+- Log2 fold change for each gene for each group, ordered according to scores. It is only provided if method is \xe2\x80\x98t-test\xe2\x80\x99 like. This is an approximation calculated from mean-log values.\n+- P-values\n+- Ajusted p-values\n+\n+This data are stored in the unstructured annotation (uns) and can be accessed using the inspect tool for AnnData objects\n+\n+More details on the `scanpy documentation\n+<https://icb-scanpy.readthedocs-hosted.com/en/stable/api/scanpy.tl.rank_genes_groups.html>`__\n \n \n-Infer progression of cells through geodesic distance along the graph (`tl.dpt`)\n-===============================================================================\n+Calculate an overlap score between data-deriven marker genes and provided markers (`tl.marker_gene_overlap`)\n+============================================================================================================\n \n-Reconstruct the progression of a biological process from snapshot\n-data. `Diffusion Pseudotime` has been introduced by Haghverdi et al (2016) and\n-implemented within Scanpy (Wolf et al, 2017). Here, we use a further developed\n-version, which is able to deal with disconnected graphs (Wolf et al, 2017) and can\n-be run in a `hierarchical` mode by setting the parameter\n-`n_branchings>1`. We recommend, however, to only use\n-`tl.dpt` for computing pseudotime (`n_branchings=0`) and\n-to detect branchings via `paga`. For pseudotime, you need\n-to annotate your data with a root cell. \n-\n-This requires to run `pp.neighbors`, first. In order to\n-reproduce the original implementation of DPT, use `method==\'gauss\'` in\n-this. Using the default `method==\'umap\'` only leads to minor quantitative\n-differences, though.\n+Marker gene overlap scores can be quoted as overlap counts, overlap coefficients, or jaccard indices. The method returns a pandas dataframe which can be used to annotate clusters based on marker gene overlaps.\n \n \n-If `n_branchings==0`, no field `dpt_groups` will be written.\n+Logarithmize the data matrix (`pp.log1p`)\n+=========================================\n \n-- dpt_pseudotime : Array of dim (number of samples) that stores the pseudotime of each cell, that is, the DPT distance with respect to the root cell.\n-- dpt_groups : Array of dim (number of samples) that stores the subgroup id (\'0\',\'1\', ...) for each cell. The groups typically correspond to \'progenitor cells\', \'undecided cells\' or \'branches\' of a process.\n+More details on the `scanpy documentation\n+<https://icb-scanpy.readthedocs-hosted.com/en/stable/api/scanpy.pp.log1p.html>`__\n \n-The tool is similar to the R package `destiny` of Angerer et al (2016).\n+Scale data to unit variance and zero mean (`pp.scale`)\n+======================================================\n \n-More details on the `tl.dpt scanpy documentation\n-<https://scanpy.readthedocs.io/en/latest/api/scanpy.api.tl.dpt.html#scanpy.api.tl.dpt>`_\n+More details on the `scanpy documentation\n+<https://icb-scanpy.readthedocs-hosted.com/en/stable/api/scanpy.pp.scale.html>`__\n \n+Computes the square root the data matrix (`pp.sqrt`)\n+====================================================\n+\n+`X = sqrt(X)`\n ]]></help>\n <expand macro="citations"/>\n </tool>\n\\ No newline at end of file\n' |
| b |
| diff -r 5d2e17328afe -r a755eaa1cc32 macros.xml --- a/macros.xml Mon Mar 04 10:15:38 2019 -0500 +++ b/macros.xml Wed Oct 16 06:31:52 2019 -0400 |
| [ |
| b'@@ -1,10 +1,12 @@\n <macros>\n- <token name="@version@">1.4</token>\n+ <token name="@version@">1.4.4</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+ <requirement type="package" version="2.9.0">h5py</requirement>\n+ <requirement type="package" version="0.7.0">leidenalg</requirement>\n <yield />\n </requirements>\n </xml>\n@@ -14,102 +16,33 @@\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+ <version_command><![CDATA[python -c "import scanpy as sc;print(\'scanpy version: %s\' % sc.__version__)"]]></version_command>\n </xml>\n <token name="@CMD@"><![CDATA[\n+cp \'$adata\' \'anndata.h5ad\' &&\n cat \'$script_file\' &&\n-python \'$script_file\'\n+python \'$script_file\' &&\n+ls .\n ]]>\n </token>\n <token name="@CMD_imports@"><![CDATA[\n-import scanpy.api as sc\n+import scanpy 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+ <param name="adata" type="data" format="h5ad" label="Annotated data matrix"/>\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+adata = sc.read(\'anndata.h5ad\')\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 '..b'tegorical for which `tl.paga` has been computed."/>\n- <param argument="layout" type="select" value="" label="Plotting layout" help="">\n- <option value="fa">fa: ForceAtlas2</option>\n- <option value="fr">fr: Fruchterman-Reingold</option>\n- <option value="fr">rt: stands for Reingold Tilford</option>\n- <option value="fr">eq_tree: equally spaced tree</option>\n- </param>\n+ <expand macro="param_layout"/>\n <param argument="init_pos" type="data" format="tabular,csv,tsv" optional="true" label="Two-column tabular file storing the x and y coordinates for initializing the layout" help=""/>\n- <param argument="random_state" type="integer" value="0" label="Random state" help="For layouts with random initialization like \'fr\', change this to use different intial states for the optimization. If `None`, the initial state is not reproducible."/>\n- <param argument="root" type="text" value="" label="Comma-separated roots" help="If choosing a tree layout, this is the index of the root node or a list of root node indices. If this is a non-empty vector then the supplied node IDs are used as the roots of the trees (or a single tree if the graph is connected). If this is `None` or an empty list, the root vertices are automatically calculated based on topological sorting."/>\n+ <expand macro="param_random_state"/>\n+ <expand macro="param_root"/>\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="solid_edges" type="text" value="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@@ -1031,10 +972,11 @@\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 str($method.color) != \'\'\n+ #set $color=([x.strip() for x in str($method.color).split(\',\')])\n+ color=$color,\n+#end if\n #if $method.pos\n pos=np.fromfile($method.pos, dtype=dt),\n #end if\n@@ -1081,4 +1023,10 @@\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+ <xml name="gene_symbols">\n+ <param argument="gene_symbols" type="text" value="" optional="true" label="Key for field in `.var` that stores gene symbols"/>\n+ </xml>\n+ <xml name="n_genes">\n+ <param argument="n_genes" type="integer" min="0" value="20" label="Number of genes to show" help=""/>\n+ </xml> \n </macros>\n' |
| b |
| diff -r 5d2e17328afe -r a755eaa1cc32 test-data/blobs.h5ad |
| b |
| Binary file test-data/blobs.h5ad has changed |
| b |
| diff -r 5d2e17328afe -r a755eaa1cc32 test-data/pl.clustermap.krumsiek11.png |
| b |
| Binary file test-data/pl.clustermap.krumsiek11.png has changed |
| b |
| diff -r 5d2e17328afe -r a755eaa1cc32 test-data/pl.dotplot.krumsiek11.png |
| b |
| Binary file test-data/pl.dotplot.krumsiek11.png has changed |
| b |
| diff -r 5d2e17328afe -r a755eaa1cc32 test-data/pl.draw_graph.png |
| b |
| Binary file test-data/pl.draw_graph.png has changed |
| b |
| diff -r 5d2e17328afe -r a755eaa1cc32 test-data/pl.highly_variable_genes.seurat.blobs.png |
| b |
| Binary file test-data/pl.highly_variable_genes.seurat.blobs.png has changed |
| b |
| diff -r 5d2e17328afe -r a755eaa1cc32 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 5d2e17328afe -r a755eaa1cc32 test-data/pl.rank_genes_groups.rank_genes_groups.krumsiek11.png |
| b |
| Binary file test-data/pl.rank_genes_groups.rank_genes_groups.krumsiek11.png has changed |
| b |
| diff -r 5d2e17328afe -r a755eaa1cc32 test-data/pl.rank_genes_groups_violin.Ery.png |
| b |
| Binary file test-data/pl.rank_genes_groups_violin.Ery.png has changed |
| b |
| diff -r 5d2e17328afe -r a755eaa1cc32 test-data/pl.rank_genes_groups_violin.Mk.png |
| b |
| Binary file test-data/pl.rank_genes_groups_violin.Mk.png has changed |
| b |
| diff -r 5d2e17328afe -r a755eaa1cc32 test-data/pl.rank_genes_groups_violin.Mo.png |
| b |
| Binary file test-data/pl.rank_genes_groups_violin.Mo.png has changed |
| b |
| diff -r 5d2e17328afe -r a755eaa1cc32 test-data/pl.rank_genes_groups_violin.Neu.png |
| b |
| Binary file test-data/pl.rank_genes_groups_violin.Neu.png has changed |
| b |
| diff -r 5d2e17328afe -r a755eaa1cc32 test-data/pl.rank_genes_groups_violin.progenitor.png |
| b |
| Binary file test-data/pl.rank_genes_groups_violin.progenitor.png has changed |
| b |
| diff -r 5d2e17328afe -r a755eaa1cc32 test-data/pl.scatter.krumsiek11.png |
| b |
| Binary file test-data/pl.scatter.krumsiek11.png has changed |
| b |
| diff -r 5d2e17328afe -r a755eaa1cc32 test-data/pl.scatter.umap.pbmc68k_reduced.png |
| b |
| Binary file test-data/pl.scatter.umap.pbmc68k_reduced.png has changed |
| b |
| diff -r 5d2e17328afe -r a755eaa1cc32 test-data/pl.stacked_violin.krumsiek11.png |
| b |
| Binary file test-data/pl.stacked_violin.krumsiek11.png has changed |
| b |
| diff -r 5d2e17328afe -r a755eaa1cc32 test-data/pp.calculate_qc_metrics.sparce_csr_matrix.h5ad |
| b |
| Binary file test-data/pp.calculate_qc_metrics.sparce_csr_matrix.h5ad has changed |
| b |
| diff -r 5d2e17328afe -r a755eaa1cc32 test-data/pp.combat.blobs.h5ad |
| b |
| Binary file test-data/pp.combat.blobs.h5ad has changed |
| b |
| diff -r 5d2e17328afe -r a755eaa1cc32 test-data/pp.downsample_counts.random-randint.h5ad |
| b |
| Binary file test-data/pp.downsample_counts.random-randint.h5ad has changed |
| b |
| diff -r 5d2e17328afe -r a755eaa1cc32 test-data/pp.filter_cells.krumsiek11-max_genes.h5ad |
| b |
| Binary file test-data/pp.filter_cells.krumsiek11-max_genes.h5ad has changed |
| b |
| diff -r 5d2e17328afe -r a755eaa1cc32 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 5d2e17328afe -r a755eaa1cc32 test-data/pp.filter_cells.number_per_cell.krumsiek11-max_genes.tabular --- a/test-data/pp.filter_cells.number_per_cell.krumsiek11-max_genes.tabular Mon Mar 04 10:15:38 2019 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| b'@@ -1,641 +0,0 @@\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 5d2e17328afe -r a755eaa1cc32 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 5d2e17328afe -r a755eaa1cc32 test-data/pp.filter_genes.number_per_gene.krumsiek11-min_counts.tabular --- a/test-data/pp.filter_genes.number_per_gene.krumsiek11-min_counts.tabular Mon Mar 04 10:15:38 2019 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,12 +0,0 @@ -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 5d2e17328afe -r a755eaa1cc32 test-data/pp.filter_genes.number_per_gene.pbmc68k_reduced-max_cells.tabular --- a/test-data/pp.filter_genes.number_per_gene.pbmc68k_reduced-max_cells.tabular Mon Mar 04 10:15:38 2019 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,222 +0,0 @@ - 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 5d2e17328afe -r a755eaa1cc32 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 5d2e17328afe -r a755eaa1cc32 test-data/pp.filter_genes_dispersion.per_gene.krumsiek11-cell_ranger.tabular --- a/test-data/pp.filter_genes_dispersion.per_gene.krumsiek11-cell_ranger.tabular Mon Mar 04 10:15:38 2019 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,12 +0,0 @@ - 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 5d2e17328afe -r a755eaa1cc32 test-data/pp.filter_genes_dispersion.per_gene.krumsiek11-seurat.tabular --- a/test-data/pp.filter_genes_dispersion.per_gene.krumsiek11-seurat.tabular Mon Mar 04 10:15:38 2019 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,9 +0,0 @@ -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 5d2e17328afe -r a755eaa1cc32 test-data/pp.filter_rank_genes_groups.h5ad |
| b |
| Binary file test-data/pp.filter_rank_genes_groups.h5ad has changed |
| b |
| diff -r 5d2e17328afe -r a755eaa1cc32 test-data/pp.highly_variable_genes.krumsiek11-cell_ranger.h5ad |
| b |
| Binary file test-data/pp.highly_variable_genes.krumsiek11-cell_ranger.h5ad has changed |
| b |
| diff -r 5d2e17328afe -r a755eaa1cc32 test-data/pp.highly_variable_genes.seurat.blobs.h5ad |
| b |
| Binary file test-data/pp.highly_variable_genes.seurat.blobs.h5ad has changed |
| b |
| diff -r 5d2e17328afe -r a755eaa1cc32 test-data/pp.log1p.krumsiek11.h5ad |
| b |
| Binary file test-data/pp.log1p.krumsiek11.h5ad has changed |
| b |
| diff -r 5d2e17328afe -r a755eaa1cc32 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 5d2e17328afe -r a755eaa1cc32 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 5d2e17328afe -r a755eaa1cc32 test-data/pp.normalize_per_cell.obs.krumsiek11.tabular --- a/test-data/pp.normalize_per_cell.obs.krumsiek11.tabular Mon Mar 04 10:15:38 2019 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,641 +0,0 @@ -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 5d2e17328afe -r a755eaa1cc32 test-data/pp.normalize_total.krumsiek11.h5ad |
| b |
| Binary file test-data/pp.normalize_total.krumsiek11.h5ad has changed |
| b |
| diff -r 5d2e17328afe -r a755eaa1cc32 test-data/pp.pca.krumsiek11.h5ad |
| b |
| Binary file test-data/pp.pca.krumsiek11.h5ad has changed |
| b |
| diff -r 5d2e17328afe -r a755eaa1cc32 test-data/pp.recipe_seurat.recipe_zheng17.h5ad |
| b |
| Binary file test-data/pp.recipe_seurat.recipe_zheng17.h5ad has changed |
| b |
| diff -r 5d2e17328afe -r a755eaa1cc32 test-data/pp.recipe_weinreb17.paul15_subsample.updated.h5ad |
| b |
| Binary file test-data/pp.recipe_weinreb17.paul15_subsample.updated.h5ad has changed |
| b |
| diff -r 5d2e17328afe -r a755eaa1cc32 test-data/pp.recipe_zheng17.random-randint.h5ad |
| b |
| Binary file test-data/pp.recipe_zheng17.random-randint.h5ad has changed |
| b |
| diff -r 5d2e17328afe -r a755eaa1cc32 test-data/pp.regress_out.krumsiek11.h5ad |
| b |
| Binary file test-data/pp.regress_out.krumsiek11.h5ad has changed |
| b |
| diff -r 5d2e17328afe -r a755eaa1cc32 test-data/pp.scale.krumsiek11.h5ad |
| b |
| Binary file test-data/pp.scale.krumsiek11.h5ad has changed |
| b |
| diff -r 5d2e17328afe -r a755eaa1cc32 test-data/pp.scale_max_value.krumsiek11.h5ad |
| b |
| Binary file test-data/pp.scale_max_value.krumsiek11.h5ad has changed |
| b |
| diff -r 5d2e17328afe -r a755eaa1cc32 test-data/pp.sqrt.krumsiek11.h5ad |
| b |
| Binary file test-data/pp.sqrt.krumsiek11.h5ad has changed |
| b |
| diff -r 5d2e17328afe -r a755eaa1cc32 test-data/pp.subsample.krumsiek11_fraction.h5ad |
| b |
| Binary file test-data/pp.subsample.krumsiek11_fraction.h5ad has changed |
| b |
| diff -r 5d2e17328afe -r a755eaa1cc32 test-data/sparce_csr_matrix.h5ad |
| b |
| Binary file test-data/sparce_csr_matrix.h5ad has changed |
| b |
| diff -r 5d2e17328afe -r a755eaa1cc32 test-data/tl.diffmap.neighbors_gauss_braycurtis.recipe_weinreb17.paul15_subsample.X_diffmap.tabular --- a/test-data/tl.diffmap.neighbors_gauss_braycurtis.recipe_weinreb17.paul15_subsample.X_diffmap.tabular Mon Mar 04 10:15:38 2019 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| b'@@ -1,100 +0,0 @@\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 5d2e17328afe -r a755eaa1cc32 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 5d2e17328afe -r a755eaa1cc32 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 5d2e17328afe -r a755eaa1cc32 test-data/tl.dpt.diffmap.neighbors_gauss_braycurtis.recipe_weinreb17.paul15_subsample.obs.tabular --- a/test-data/tl.dpt.diffmap.neighbors_gauss_braycurtis.recipe_weinreb17.paul15_subsample.obs.tabular Mon Mar 04 10:15:38 2019 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,101 +0,0 @@ -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 5d2e17328afe -r a755eaa1cc32 test-data/tl.draw_graph.pp.neighbors_umap_euclidean.recipe_weinreb17.paul15_subsample.h5ad |
| b |
| Binary file test-data/tl.draw_graph.pp.neighbors_umap_euclidean.recipe_weinreb17.paul15_subsample.h5ad has changed |
| b |
| diff -r 5d2e17328afe -r a755eaa1cc32 test-data/tl.leiden.neighbors_gauss_braycurtis.recipe_weinreb17.paul15_subsample.h5ad |
| b |
| Binary file test-data/tl.leiden.neighbors_gauss_braycurtis.recipe_weinreb17.paul15_subsample.h5ad has changed |
| b |
| diff -r 5d2e17328afe -r a755eaa1cc32 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 5d2e17328afe -r a755eaa1cc32 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 5d2e17328afe -r a755eaa1cc32 test-data/tl.pca.krumsiek11.h5ad |
| b |
| Binary file test-data/tl.pca.krumsiek11.h5ad has changed |
| b |
| diff -r 5d2e17328afe -r a755eaa1cc32 test-data/tl.rank_genes_groups.krumsiek11.h5ad |
| b |
| Binary file test-data/tl.rank_genes_groups.krumsiek11.h5ad has changed |
| b |
| diff -r 5d2e17328afe -r a755eaa1cc32 test-data/tl.rank_genes_groups.liblinear.krumsiek11.h5ad |
| b |
| Binary file test-data/tl.rank_genes_groups.liblinear.krumsiek11.h5ad has changed |
| b |
| diff -r 5d2e17328afe -r a755eaa1cc32 test-data/tl.rank_genes_groups.newton-cg.pbmc68k_reduced.h5ad |
| b |
| Binary file test-data/tl.rank_genes_groups.newton-cg.pbmc68k_reduced.h5ad has changed |
| b |
| diff -r 5d2e17328afe -r a755eaa1cc32 test-data/tl.score_genes.krumsiek11.h5ad |
| b |
| Binary file test-data/tl.score_genes.krumsiek11.h5ad has changed |
| b |
| diff -r 5d2e17328afe -r a755eaa1cc32 test-data/tl.score_genes.krumsiek11.obs.tabular --- a/test-data/tl.score_genes.krumsiek11.obs.tabular Mon Mar 04 10:15:38 2019 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| b'@@ -1,641 +0,0 @@\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 5d2e17328afe -r a755eaa1cc32 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 5d2e17328afe -r a755eaa1cc32 test-data/tl.score_genes_cell_cycle.krumsiek11.obs.tabular --- a/test-data/tl.score_genes_cell_cycle.krumsiek11.obs.tabular Mon Mar 04 10:15:38 2019 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| b'@@ -1,641 +0,0 @@\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 5d2e17328afe -r a755eaa1cc32 test-data/tl.tsne.krumsiek11.h5ad |
| b |
| Binary file test-data/tl.tsne.krumsiek11.h5ad has changed |
| b |
| diff -r 5d2e17328afe -r a755eaa1cc32 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 |
