Repository revision
8:6adf98e782f3

Repository 'scanpy_plot'
hg clone https://toolshed.g2.bx.psu.edu/repos/iuc/scanpy_plot

Plot tool metadata
Miscellaneous
Plot
with scanpy
scanpy_plot
toolshed.g2.bx.psu.edu/repos/iuc/scanpy_plot/scanpy_plot/1.7.1+galaxy0
1.7.1+galaxy0
python -c "import scanpy as sc;print('scanpy version: %s' % sc.__version__)"
True
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