Miscellaneous |
Version lineage of this tool (guids ordered most recent to oldest) |
toolshed.g2.bx.psu.edu/repos/iuc/scanpy_plot/scanpy_plot/1.4.4.post1+galaxy3 |
toolshed.g2.bx.psu.edu/repos/iuc/scanpy_plot/scanpy_plot/1.4.4.post1+galaxy2 (this tool) |
toolshed.g2.bx.psu.edu/repos/iuc/scanpy_plot/scanpy_plot/1.4.4.post1+galaxy1 |
toolshed.g2.bx.psu.edu/repos/iuc/scanpy_plot/scanpy_plot/1.4.4.post1+galaxy0 |
toolshed.g2.bx.psu.edu/repos/iuc/scanpy_plot/scanpy_plot/1.4.4+galaxy0 |
toolshed.g2.bx.psu.edu/repos/iuc/scanpy_plot/scanpy_plot/1.4+galaxy0 |
scanpy_plot |
Requirements (dependencies defined in the <requirements> tag set) |
name | version | type |
scanpy | 1.4.4.post1 | package |
loompy | 2.0.17 | package |
h5py | 2.9.0 | package |
leidenalg | 0.7.0 | package |
Functional tests |
name | inputs | outputs | required files |
Test-1 |
advanced_common|show_log: True method|type|type: basis adata: pbmc68k_reduced.h5ad method|plot|size: 1 method|sort_order: True method|plot|palette: inferno format: png method|use_raw: True method|plot|legend_fontsize: 1 method|type|basis: umap method|method: pl.scatter method|type|color: HES4 method|plot|legend_loc: right margin method|plot|color_map: inferno method|plot|legend_fontweight: normal method|plot|projection: 2d method|plot|frameon: True |
attributes: name attributes: name |
pbmc68k_reduced.h5ad name |
Test-2 |
advanced_common|show_log: True adata: krumsiek11.h5ad format: png method|sort_order: True method|plot|palette: bwr method|method: pl.scatter method|type|layers|use_layers: false method|plot|title: A title method|use_raw: False method|plot|legend_fontweight: normal method|plot|legend_fontsize: 1 method|plot|frameon: False method|plot|size: 1 method|plot|legend_loc: right margin method|plot|projection: 2d method|type|type: xy method|type|x: EKLF method|type|y: Cebpa |
attributes: name attributes: name |
krumsiek11.h5ad name |
Test-3 |
method|matplotlib_pyplot_imshow|interpolation: None advanced_common|show_log: True method|groupby: cell_type method|method: pl.heatmap format: png method|log: False method|figsize|width: 10 method|matplotlib_pyplot_imshow|origin: upper method|dendrogram: True method|swap_axes: True method|var_names|type: all method|show_gene_labels: False method|figsize|height: 3 method|matplotlib_pyplot_imshow|cmap: YlGnBu method|use_raw: False method|num_categories: 7 adata: krumsiek11.h5ad method|figsize|test: yes |
attributes: name attributes: name |
krumsiek11.h5ad name |
Test-4 |
method|dot_min: 0.1 method|dot_max: 0.7 method|matplotlib_pyplot_scatter|linewidths: 0 method|figsize|test: no method|num_categories: 7 advanced_common|show_log: True method|groupby: louvain method|var_group_positions_0|end: 1 method|var_group_positions_0|label: B cells format: png method|var_group_positions_0|start: 0 method|var_names|var_names: CD79A, MS4A1, CD8A, CD8B, LYZ, GNLY, NKG7, RP3-467N11.1, FCGR3A, FCER1A, CST3, POU2AF1, LINC00402 method|matplotlib_pyplot_scatter|edgecolors: face method|log: False method|color_map: hot method|var_group_positions_1|start: 11 method|use_raw: False method|var_group_positions_1|label: dendritic method|var_group_positions_1|end: 12 method|dendrogram: True adata: pbmc68k_reduced.h5ad method|method: pl.dotplot method|var_names|type: custom |
attributes: name attributes: name |
pbmc68k_reduced.h5ad name |
Test-5 |
method|seaborn_violinplot|bw: scott advanced_common|show_log: True method|violin_plot|multi_panel|multi_panel: True method|log: False method|key_variables|type: custom format: png method|method: pl.violin method|key_variables|keys: n_genes, percent_mito, n_counts method|violin_plot|stripplot|stripplot: True method|use_raw: False method|seaborn_violinplot|saturation: 0.75 method|violin_plot|multi_panel|width: 20 method|violin_plot|multi_panel|height: 20 method|violin_plot|scale: width method|seaborn_violinplot|palette: viridis adata: pbmc68k_reduced.h5ad method|seaborn_violinplot|linewidth: 0 method|seaborn_violinplot|color: AliceBlue |
attributes: name attributes: name |
pbmc68k_reduced.h5ad name |
Test-6 |
method|seaborn_violinplot|bw: scott advanced_common|show_log: True method|groupby: cell_type method|standard_scale: None method|log: False method|method: pl.stacked_violin method|seaborn_violinplot|color: AliceBlue format: png method|violin_plot|stripplot|stripplot: True method|dendrogram: True method|swap_axes: True method|row_palette: muted method|var_names|type: all method|figsize|test: no method|violin_plot|scale: width method|seaborn_violinplot|palette: viridis method|use_raw: False method|num_categories: 7 adata: krumsiek11.h5ad method|seaborn_violinplot|linewidth: 0 method|seaborn_violinplot|saturation: 0.75 |
attributes: name attributes: name |
krumsiek11.h5ad name |
Test-7 |
advanced_common|show_log: True method|groupby: cell_type method|log: False format: png method|use_raw: False method|method: pl.matrixplot method|matplotlib_pyplot_pcolor|edgecolors: face method|swap_axes: True method|var_names|type: all method|figsize|test: no method|matplotlib_pyplot_pcolor|cmap: viridis method|num_categories: 7 method|dendrogram: True adata: krumsiek11.h5ad method|matplotlib_pyplot_pcolor|snap: False |
attributes: name attributes: name |
krumsiek11.h5ad name |
Test-8 |
method|seaborn_clustermap|z_score: None method|seaborn_clustermap|standard_scale: None method|method: pl.clustermap method|seaborn_clustermap|method: single format: png advanced_common|show_log: True method|seaborn_clustermap|col_cluster: False method|use_raw: False method|seaborn_clustermap|row_cluster: False method|seaborn_clustermap|metric: euclidean adata: krumsiek11.h5ad |
attributes: name attributes: name |
krumsiek11.h5ad name |
Test-9 |
advanced_common|show_log: True method|method: pl.highest_expr_genes method|n_top: 30 method|setseaborn_boxplot|saturation: 0.5 format: png method|gene_symbols: means method|setseaborn_boxplot|color: blue adata: pp.filter_genes_dispersion.krumsiek11-seurat.h5ad |
attributes: name attributes: name |
pp.filter_genes_dispersion.krumsiek11-seurat.h5ad name |
Test-10 |
method|highly_variable_genes: True advanced_common|show_log: True format: png method|method: pl.highly_variable_genes method|log: False adata: pp.highly_variable_genes.seurat.blobs.h5ad |
attributes: name attributes: name |
pp.highly_variable_genes.seurat.blobs.h5ad name |
Test-11 |
method|plot|size: 1 method|matplotlib_pyplot_scatter|linewidths: 0 method|plot|legend_loc: right margin method|plot|legend_fontweight: normal method|plot|components_1|axis2: 3 method|plot|components_1|axis1: 1 advanced_common|show_log: True method|plot|hspace: 0.25 method|plot|ncols: 2 method|method: pl.pca method|plot|frameon: True method|color: CD3D,CD79A method|matplotlib_pyplot_scatter|edgecolors: face format: pdf method|sort_order: True method|use_raw: False method|plot|legend_fontsize: 1 method|plot|components_0|axis2: 2 method|plot|components_0|axis1: 1 adata: pbmc68k_reduced.h5ad method|plot|projection: 2d method|plot|wspace: 0.1 method|plot|palette: viridis |
attributes: name attributes: name |
pbmc68k_reduced.h5ad name |
Test-12 |
method|components: 1,2,3 advanced_common|show_log: True format: png adata: pp.pca.krumsiek11.h5ad method|method: pl.pca_loadings |
attributes: name attributes: name |
pp.pca.krumsiek11.h5ad name |
Test-13 |
advanced_common|show_log: True format: png method|method: pl.pca_variance_ratio method|log: False method|n_pcs: 5 adata: pp.pca.krumsiek11.h5ad |
attributes: name attributes: name |
pp.pca.krumsiek11.h5ad name |
Test-14 |
advanced_common|show_log: True method|plot|hspace: 0.25 adata: pp.pca.krumsiek11.h5ad method|plot|ncols: 4 format: png method|sort_order: True method|plot|palette: viridis method|plot|size: 1 method|use_raw: False method|plot|legend_fontsize: 1 method|method: pl.pca_overview method|plot|legend_loc: right margin method|plot|wspace: 0.1 method|plot|frameon: True method|plot|legend_fontweight: normal method|plot|projection: 2d |
attributes: name attributes: name |
pp.pca.krumsiek11.h5ad name |
Test-15 |
advanced_common|show_log: True method|plot|hspace: 0.25 method|edges|edges: False method|plot|ncols: 4 format: png method|sort_order: True method|arrows: False method|method: pl.tsne method|plot|palette: viridis method|use_raw: False method|plot|legend_fontweight: normal method|plot|legend_fontsize: 1 method|plot|frameon: True method|plot|size: 1 method|plot|legend_loc: right margin method|plot|wspace: 0.1 method|matplotlib_pyplot_scatter|linewidths: 0 adata: tl.tsne.krumsiek11.h5ad method|plot|projection: 2d method|matplotlib_pyplot_scatter|edgecolors: face |
attributes: name attributes: name |
tl.tsne.krumsiek11.h5ad name |
Test-16 |
method|edges|edges: True method|plot|size: 1 method|arrows: False method|matplotlib_pyplot_scatter|linewidths: 0 method|edges|edges_color: AliceBlue method|plot|legend_loc: right margin method|plot|legend_fontweight: normal method|color: paul15_clusters advanced_common|show_log: True method|plot|hspace: 0.25 method|plot|ncols: 4 method|method: pl.umap method|plot|frameon: True method|matplotlib_pyplot_scatter|edgecolors: face method|edges|edges_width: 0.1 format: png method|use_raw: False method|plot|legend_fontsize: 1 adata: tl.umap.neighbors_umap_euclidean.recipe_weinreb17.paul15_subsample.h5ad method|plot|projection: 2d method|plot|wspace: 0.1 method|plot|palette: viridis |
attributes: name attributes: name |
tl.umap.neighbors_umap_euclidean.recipe_weinreb17.paul15_subsample.h5ad name |
Test-17 |
advanced_common|show_log: True method|plot|hspace: 0.25 method|matplotlib_pyplot_scatter|edgecolors: face method|plot|ncols: 4 format: png method|sort_order: True method|plot|palette: viridis method|method: pl.diffmap method|use_raw: False adata: tl.diffmap.neighbors_gauss_braycurtis.recipe_weinreb17.paul15_subsample.h5ad method|plot|legend_fontsize: 1 method|plot|size: 1 method|plot|legend_loc: right margin method|plot|wspace: 0.1 method|plot|frameon: True method|plot|legend_fontweight: normal method|plot|projection: 2d method|color: paul15_clusters method|matplotlib_pyplot_scatter|linewidths: 0 |
attributes: name attributes: name |
tl.diffmap.neighbors_gauss_braycurtis.recipe_weinreb17.paul15_subsample.h5ad name |
Test-18 |
advanced_common|show_log: True method|plot|frameon: True method|plot|hspace: 0.25 method|edges|edges: True method|edges|edges_width: 0.1 format: png method|sort_order: False method|arrows: False method|method: pl.draw_graph method|plot|palette: viridis method|use_raw: False method|plot|legend_fontweight: normal method|plot|wspace: 0.1 method|edges|edges_color: Crimson method|plot|legend_loc: right margin method|plot|ncols: 4 method|matplotlib_pyplot_scatter|linewidths: 0 adata: tl.draw_graph.pp.neighbors_umap_euclidean.recipe_weinreb17.paul15_subsample.h5ad method|plot|projection: 2d method|matplotlib_pyplot_scatter|edgecolors: face |
attributes: name attributes: name |
tl.draw_graph.pp.neighbors_umap_euclidean.recipe_weinreb17.paul15_subsample.h5ad name |
Test-19 |
advanced_common|show_log: True format: png method|method: pl.dpt_timeseries method|heatmap|as_heatmap: True method|heatmap|color_map: viridis adata: tl.dpt.diffmap.neighbors_gauss_braycurtis.recipe_weinreb17.paul15_subsample.h5ad |
attributes: name attributes: name |
tl.dpt.diffmap.neighbors_gauss_braycurtis.recipe_weinreb17.paul15_subsample.h5ad name |
Test-20 |
advanced_common|show_log: True method|method: pl.rank_genes_groups method|sharey: True format: png method|n_genes: 10 method|ncols: 4 method|fontsize: 8 adata: tl.rank_genes_groups.krumsiek11.h5ad |
attributes: name attributes: name |
tl.rank_genes_groups.krumsiek11.h5ad name |
Test-21 |
advanced_common|show_log: True method|split: True method|method: pl.rank_genes_groups_violin method|genes|n_genes: 10 format: png method|violin_plot|stripplot|stripplot: True method|use_raw: False method|genes|select: n_genes method|violin_plot|scale: width adata: tl.rank_genes_groups.krumsiek11.h5ad |
attributes: name |
tl.rank_genes_groups.krumsiek11.h5ad name |
Test-22 |
advanced_common|show_log: True method|matplotlib_pyplot_scatter|edgecolors: face format: png method|color_map: viridis method|log: False method|dendrogram: False method|method: pl.rank_genes_groups_dotplot method|n_genes: 10 method|use_raw: False adata: tl.rank_genes_groups.krumsiek11.h5ad method|matplotlib_pyplot_scatter|linewidths: 0 |
attributes: name attributes: name |
tl.rank_genes_groups.krumsiek11.h5ad name |
Test-23 |
method|matplotlib_pyplot_imshow|interpolation: None advanced_common|show_log: True method|show_gene_labels: False method|log: False format: png method|method: pl.rank_genes_groups_heatmap method|matplotlib_pyplot_imshow|origin: upper method|dendrogram: False method|swap_axes: False method|n_genes: 10 method|matplotlib_pyplot_imshow|cmap: viridis method|use_raw: False adata: tl.rank_genes_groups.krumsiek11.h5ad |
attributes: name attributes: name |
tl.rank_genes_groups.krumsiek11.h5ad name |
Test-24 |
method|swap_axes: False advanced_common|show_log: True method|log: False format: png method|method: pl.rank_genes_groups_matrixplot method|use_raw: False method|matplotlib_pyplot_pcolor|edgecolors: face method|n_genes: 10 method|matplotlib_pyplot_pcolor|cmap: viridis method|matplotlib_pyplot_pcolor|snap: False method|dendrogram: False adata: tl.rank_genes_groups.krumsiek11.h5ad |
attributes: name attributes: name |
tl.rank_genes_groups.krumsiek11.h5ad name |
Test-25 |
method|seaborn_violinplot|bw: scott advanced_common|show_log: True method|standard_scale: None method|log: False format: png method|method: pl.rank_genes_groups_stacked_violin method|violin_plot|stripplot|stripplot: True method|dendrogram: True method|swap_axes: True method|row_palette: muted method|n_genes: 10 method|seaborn_violinplot|color: AliceBlue method|violin_plot|scale: width method|seaborn_violinplot|palette: viridis method|use_raw: False adata: tl.rank_genes_groups.krumsiek11.h5ad method|seaborn_violinplot|linewidth: 0 method|seaborn_violinplot|saturation: 0.75 |
attributes: name attributes: name |
tl.rank_genes_groups.krumsiek11.h5ad name |