Miscellaneous |
Version lineage of this tool (guids ordered most recent to oldest) |
toolshed.g2.bx.psu.edu/repos/iuc/scanpy_plot/scanpy_plot/1.7.1+galaxy1 |
toolshed.g2.bx.psu.edu/repos/iuc/scanpy_plot/scanpy_plot/1.7.1+galaxy0 (this tool) |
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 |
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 | 1.7.1 | package |
loompy | 2.0.17 | package |
leidenalg | 0.8.3 | package |
Functional tests |
name | inputs | outputs | required files |
Test-1 |
adata: pbmc68k_reduced.h5ad format: png method|type|basis: umap method|type|color: HES4 method|type|type: basis method|use_raw: True method|sort_order: True method|plot|projection: 2d method|plot|legend_loc: right margin method|plot|legend_fontsize: 1 method|plot|legend_fontweight: normal method|plot|color_map: inferno method|plot|palette: inferno method|plot|frameon: True method|plot|size: 1 method|method: pl.scatter advanced_common|show_log: True |
name: value name: value |
pbmc68k_reduced.h5ad value |
Test-2 |
adata: krumsiek11.h5ad format: png method|type|x: EKLF method|type|y: Cebpa method|type|layers|use_layers: false method|type|type: xy method|use_raw: False method|sort_order: True method|plot|projection: 2d method|plot|legend_loc: right margin method|plot|legend_fontsize: 1 method|plot|legend_fontweight: normal method|plot|palette: bwr method|plot|frameon: False method|plot|size: 1 method|plot|title: A title method|method: pl.scatter advanced_common|show_log: True |
name: value name: value |
krumsiek11.h5ad value |
Test-3 |
adata: krumsiek11.h5ad format: png method|var_names|type: all method|groupby: cell_type method|num_categories: 7 method|log: False method|use_raw: False method|dendrogram: True method|figsize|width: 10 method|figsize|height: 3 method|figsize|test: yes method|swap_axes: True method|show_gene_labels: False method|matplotlib_pyplot_imshow|cmap: YlGnBu method|matplotlib_pyplot_imshow|interpolation: None method|matplotlib_pyplot_imshow|origin: upper method|method: pl.heatmap advanced_common|show_log: True |
name: value name: value |
krumsiek11.h5ad value |
Test-4 |
adata: pbmc68k_reduced.h5ad format: png method|var_names|var_names: CD79A, MS4A1, CD8A, CD8B, LYZ, GNLY, NKG7, RP3-467N11.1, FCGR3A, FCER1A, CST3, POU2AF1, LINC00402 method|var_names|type: custom method|groupby: louvain method|num_categories: 7 method|log: False method|use_raw: False method|dendrogram: True method|var_group_positions_0|start: 0 method|var_group_positions_0|end: 1 method|var_group_positions_0|label: B cells method|var_group_positions_1|start: 11 method|var_group_positions_1|end: 12 method|var_group_positions_1|label: dendritic method|figsize|test: no method|color_map: hot method|dot_max: 0.7 method|dot_min: 0.1 method|matplotlib_pyplot_scatter|linewidths: 0 method|matplotlib_pyplot_scatter|edgecolors: face method|method: pl.dotplot advanced_common|show_log: True |
name: value name: value |
pbmc68k_reduced.h5ad value |
Test-5 |
adata: pbmc68k_reduced.h5ad format: png method|key_variables|keys: n_genes, percent_mito, n_counts method|key_variables|type: custom method|log: False method|use_raw: False method|violin_plot|stripplot|stripplot: True method|violin_plot|multi_panel|width: 20 method|violin_plot|multi_panel|height: 20 method|violin_plot|multi_panel|multi_panel: True method|violin_plot|scale: width method|seaborn_violinplot|bw: scott method|seaborn_violinplot|linewidth: 0 method|seaborn_violinplot|color: AliceBlue method|seaborn_violinplot|saturation: 0.75 method|method: pl.violin advanced_common|show_log: True |
name: value name: value |
pbmc68k_reduced.h5ad value |
Test-6 |
adata: krumsiek11.h5ad format: png method|var_names|type: all method|groupby: cell_type method|num_categories: 7 method|log: False method|use_raw: False method|dendrogram: True method|figsize|test: no method|swap_axes: True method|violin_plot|stripplot|stripplot: True method|violin_plot|scale: width method|row_palette: muted method|standard_scale: None method|seaborn_violinplot|bw: scott method|seaborn_violinplot|linewidth: 0 method|seaborn_violinplot|color: AliceBlue method|seaborn_violinplot|saturation: 0.75 method|method: pl.stacked_violin advanced_common|show_log: True |
name: value name: value |
krumsiek11.h5ad value |
Test-7 |
adata: krumsiek11.h5ad format: png method|var_names|type: all method|groupby: cell_type method|num_categories: 7 method|log: False method|use_raw: False method|dendrogram: True method|figsize|test: no method|swap_axes: True method|matplotlib_pyplot_pcolor|cmap: viridis method|matplotlib_pyplot_pcolor|edgecolors: face method|matplotlib_pyplot_pcolor|snap: False method|method: pl.matrixplot advanced_common|show_log: True |
name: value name: value |
krumsiek11.h5ad value |
Test-8 |
adata: krumsiek11.h5ad format: png method|use_raw: False method|seaborn_clustermap|method: single method|seaborn_clustermap|metric: euclidean method|seaborn_clustermap|z_score: None method|seaborn_clustermap|standard_scale: None method|seaborn_clustermap|col_cluster: False method|seaborn_clustermap|row_cluster: False method|method: pl.clustermap advanced_common|show_log: True |
name: value name: value |
krumsiek11.h5ad value |
Test-9 |
adata: pp.filter_genes_dispersion.krumsiek11-seurat.h5ad format: png method|n_top: 30 method|gene_symbols: means method|setseaborn_boxplot|color: blue method|setseaborn_boxplot|saturation: 0.5 method|method: pl.highest_expr_genes advanced_common|show_log: True |
name: value name: value |
pp.filter_genes_dispersion.krumsiek11-seurat.h5ad value |
Test-10 |
adata: pp.highly_variable_genes.seurat.blobs.h5ad format: png method|log: False method|highly_variable_genes: True method|method: pl.highly_variable_genes advanced_common|show_log: True |
name: value name: value |
pp.highly_variable_genes.seurat.blobs.h5ad value |
Test-11 |
adata: pbmc68k_reduced.h5ad format: pdf method|color: CD3D,CD79A method|use_raw: False method|sort_order: True method|plot|components_0|axis1: 1 method|plot|components_0|axis2: 2 method|plot|components_1|axis1: 1 method|plot|components_1|axis2: 3 method|plot|projection: 2d method|plot|legend_loc: right margin method|plot|legend_fontsize: 1 method|plot|legend_fontweight: normal method|plot|size: 1 method|plot|palette: viridis method|plot|frameon: True method|plot|ncols: 2 method|plot|wspace: 0.1 method|plot|hspace: 0.25 method|matplotlib_pyplot_scatter|linewidths: 0 method|matplotlib_pyplot_scatter|edgecolors: face method|method: pl.pca advanced_common|show_log: True |
name: value name: value |
pbmc68k_reduced.h5ad value |
Test-12 |
adata: pp.pca.krumsiek11.h5ad format: png method|components: 1,2,3 method|method: pl.pca_loadings advanced_common|show_log: True |
name: value name: value |
pp.pca.krumsiek11.h5ad value |
Test-13 |
adata: pp.pca.krumsiek11.h5ad format: png method|n_pcs: 5 method|log: False method|method: pl.pca_variance_ratio advanced_common|show_log: True |
name: value name: value |
pp.pca.krumsiek11.h5ad value |
Test-14 |
adata: pp.pca.krumsiek11.h5ad format: png method|use_raw: False method|sort_order: True method|plot|projection: 2d method|plot|legend_loc: right margin method|plot|legend_fontsize: 1 method|plot|legend_fontweight: normal method|plot|size: 1 method|plot|palette: viridis method|plot|frameon: True method|plot|ncols: 4 method|plot|wspace: 0.1 method|plot|hspace: 0.25 method|method: pl.pca_overview advanced_common|show_log: True |
name: value name: value |
pp.pca.krumsiek11.h5ad value |
Test-15 |
adata: tl.tsne.krumsiek11.h5ad format: png method|use_raw: False method|edges|edges: False method|arrows: False method|sort_order: True method|plot|projection: 2d method|plot|legend_loc: right margin method|plot|legend_fontsize: 1 method|plot|legend_fontweight: normal method|plot|size: 1 method|plot|palette: viridis method|plot|frameon: True method|plot|ncols: 4 method|plot|wspace: 0.1 method|plot|hspace: 0.25 method|matplotlib_pyplot_scatter|linewidths: 0 method|matplotlib_pyplot_scatter|edgecolors: face method|method: pl.tsne advanced_common|show_log: True |
name: value name: value |
tl.tsne.krumsiek11.h5ad value |
Test-16 |
adata: tl.umap.neighbors_umap_euclidean.recipe_weinreb17.paul15_subsample.h5ad format: png method|color: paul15_clusters method|use_raw: False method|edges|edges_width: 0.1 method|edges|edges_color: AliceBlue method|edges|edges: True method|arrows: False method|plot|projection: 2d method|plot|legend_loc: right margin method|plot|legend_fontsize: 1 method|plot|legend_fontweight: normal method|plot|size: 1 method|plot|palette: viridis method|plot|frameon: True method|plot|ncols: 4 method|plot|wspace: 0.1 method|plot|hspace: 0.25 method|matplotlib_pyplot_scatter|linewidths: 0 method|matplotlib_pyplot_scatter|edgecolors: face method|method: pl.umap advanced_common|show_log: True |
name: value name: value |
tl.umap.neighbors_umap_euclidean.recipe_weinreb17.paul15_subsample.h5ad value |
Test-17 |
adata: tl.diffmap.neighbors_gauss_braycurtis.recipe_weinreb17.paul15_subsample.h5ad format: png method|color: paul15_clusters method|use_raw: False method|sort_order: True method|plot|projection: 2d method|plot|legend_loc: right margin method|plot|legend_fontsize: 1 method|plot|legend_fontweight: normal method|plot|size: 1 method|plot|palette: viridis method|plot|frameon: True method|plot|ncols: 4 method|plot|wspace: 0.1 method|plot|hspace: 0.25 method|matplotlib_pyplot_scatter|linewidths: 0 method|matplotlib_pyplot_scatter|edgecolors: face method|method: pl.diffmap advanced_common|show_log: True |
name: value name: value |
tl.diffmap.neighbors_gauss_braycurtis.recipe_weinreb17.paul15_subsample.h5ad value |
Test-18 |
adata: tl.draw_graph.pp.neighbors_umap_euclidean.recipe_weinreb17.paul15_subsample.h5ad format: png method|use_raw: False method|layout: fr method|edges|edges_width: 0.1 method|edges|edges_color: Crimson method|edges|edges: True method|arrows: False method|sort_order: False method|plot|projection: 2d method|plot|legend_loc: right margin method|plot|legend_fontweight: normal method|plot|palette: viridis method|plot|frameon: True method|plot|ncols: 4 method|plot|wspace: 0.1 method|plot|hspace: 0.25 method|matplotlib_pyplot_scatter|linewidths: 0 method|matplotlib_pyplot_scatter|edgecolors: face method|method: pl.draw_graph advanced_common|show_log: True |
name: value name: value |
tl.draw_graph.pp.neighbors_umap_euclidean.recipe_weinreb17.paul15_subsample.h5ad value |
Test-19 |
adata: tl.dpt.diffmap.neighbors_gauss_braycurtis.recipe_weinreb17.paul15_subsample.h5ad format: png method|heatmap|color_map: viridis method|heatmap|as_heatmap: True method|method: pl.dpt_timeseries advanced_common|show_log: True |
name: value name: value |
tl.dpt.diffmap.neighbors_gauss_braycurtis.recipe_weinreb17.paul15_subsample.h5ad value |
Test-20 |
adata: tl.rank_genes_groups.krumsiek11.h5ad format: png method|n_genes: 10 method|fontsize: 8 method|ncols: 4 method|sharey: True method|method: pl.rank_genes_groups advanced_common|show_log: True |
name: value name: value |
tl.rank_genes_groups.krumsiek11.h5ad value |
Test-21 |
adata: tl.rank_genes_groups.krumsiek11.h5ad format: png method|n_genes: 10 method|log: False method|use_raw: False method|dendrogram: False method|color_map: viridis method|matplotlib_pyplot_scatter|linewidths: 0 method|matplotlib_pyplot_scatter|edgecolors: face method|method: pl.rank_genes_groups_dotplot advanced_common|show_log: True |
name: value name: value |
tl.rank_genes_groups.krumsiek11.h5ad value |
Test-22 |
adata: tl.rank_genes_groups.krumsiek11.h5ad format: png method|n_genes: 10 method|log: False method|use_raw: False method|dendrogram: False method|swap_axes: False method|show_gene_labels: False method|matplotlib_pyplot_imshow|cmap: viridis method|matplotlib_pyplot_imshow|interpolation: None method|matplotlib_pyplot_imshow|origin: upper method|method: pl.rank_genes_groups_heatmap advanced_common|show_log: True |
name: value name: value |
tl.rank_genes_groups.krumsiek11.h5ad value |
Test-23 |
adata: tl.rank_genes_groups.krumsiek11.h5ad format: png method|n_genes: 10 method|log: False method|use_raw: False method|dendrogram: False method|swap_axes: False method|matplotlib_pyplot_pcolor|cmap: viridis method|matplotlib_pyplot_pcolor|edgecolors: face method|matplotlib_pyplot_pcolor|snap: False method|method: pl.rank_genes_groups_matrixplot advanced_common|show_log: True |
name: value name: value |
tl.rank_genes_groups.krumsiek11.h5ad value |
Test-24 |
adata: tl.rank_genes_groups.krumsiek11.h5ad format: png method|n_genes: 10 method|log: False method|use_raw: False method|dendrogram: True method|swap_axes: True method|violin_plot|stripplot|stripplot: True method|violin_plot|scale: width method|row_palette: muted method|standard_scale: None method|seaborn_violinplot|bw: scott method|seaborn_violinplot|linewidth: 0 method|seaborn_violinplot|color: AliceBlue method|seaborn_violinplot|saturation: 0.75 method|method: pl.rank_genes_groups_stacked_violin advanced_common|show_log: True |
name: value name: value |
tl.rank_genes_groups.krumsiek11.h5ad value |