Repository revision
6:dbbe1ea8ecb1

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/1.4.4.post1+galaxy2
1.4.4.post1+galaxy2
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/1.4.4.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