Mercurial > repos > iuc > scanpy_plot

changeset 14:f7446fd8d5e7 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 9d49b2a98de059ae9a053dc1c5a23537cf0311de
author iuc
date Sat, 18 May 2024 18:32:22 +0000
parents 6f5349dd5c49
children 70fa84e99463
files macros.xml plot.xml
diffstat 2 files changed, 24 insertions(+), 24 deletions(-) [+]
line wrap: on
line diff
--- a/macros.xml	Thu Mar 14 15:35:53 2024 +0000
+++ b/macros.xml	Sat May 18 18:32:22 2024 +0000
@@ -1,7 +1,7 @@
 <macros>
     <token name="@TOOL_VERSION@">1.9.6</token>
-    <token name="@VERSION_SUFFIX@">2</token>
-    <token name="@profile@">22.05</token>
+    <token name="@VERSION_SUFFIX@">3</token>
+    <token name="@profile@">21.09</token>
     <xml name="requirements">
         <requirements>
             <requirement type="package" version="@TOOL_VERSION@">scanpy</requirement>
--- a/plot.xml	Thu Mar 14 15:35:53 2024 +0000
+++ b/plot.xml	Sat May 18 18:32:22 2024 +0000
@@ -2299,7 +2299,7 @@
 category.
 
 More details on the `scanpy documentation
-<https://icb-scanpy.readthedocs-hosted.com/en/stable/api/scanpy.pl.matrixplot.html>`__
+<https://scanpy.readthedocs.io/en/stable/api/scanpy.pl.matrixplot.html>`__
 
 Generic: Hierarchically-clustered heatmap (`pl.clustermap`)
 ===========================================================
@@ -2317,7 +2317,7 @@
 Column indices, use: clustergrid.dendrogram_col.reordered_ind
 
 More details on the `scanpy documentation
-<https://icb-scanpy.readthedocs-hosted.com/en/stable/api/scanpy.pl.clustermap.html>`__
+<https://scanpy.readthedocs.io/en/stable/api/scanpy.pl.clustermap.html>`__
 
 Preprocessing: Plot the fraction of counts assigned to each gene over all cells (`pl.highest_expr_genes`)
 =========================================================================================================
@@ -2329,7 +2329,7 @@
 This plot is similar to the `scater` package function `plotHighestExprs(type= "highest-expression")`
 
 More details on the `scanpy documentation
-<https://icb-scanpy.readthedocs-hosted.com/en/stable/api/scanpy.pl.highest_expr_genes.html>`__
+<https://scanpy.readthedocs.io/en/stable/api/generated/scanpy.pl.highest_expr_genes.html>`__
 
 Preprocessing: Plot dispersions versus means for genes (`pl.highly_variable_genes`)
 ===================================================================================
@@ -2337,25 +2337,25 @@
 It produces Supp. Fig. 5c of Zheng et al. (2017) and MeanVarPlot() of Seurat.
 
 More details on the `scanpy documentation
-<https://icb-scanpy.readthedocs-hosted.com/en/stable/api/scanpy.pl.highly_variable_genes.html>`__
+<https://scanpy.readthedocs.io/en/stable/api/generated/scanpy.pl.highly_variable_genes.html>`__
 
 PCA: Scatter plot in PCA coordinates (`pl.pca`)
 ===============================================
 
 More details on the `scanpy documentation
-<https://icb-scanpy.readthedocs-hosted.com/en/stable/api/scanpy.pl.pca.html>`__
+<https://scanpy.readthedocs.io/en/stable/api/generated/scanpy.pl.pca.html>`__
 
 PCA: Rank genes according to contributions to PCs (`pl.pca_loadings`)
 =====================================================================
 
 More details on the `scanpy documentation
-<https://icb-scanpy.readthedocs-hosted.com/en/stable/api/scanpy.pl.pca_loadings.html>`__
+<https://scanpy.readthedocs.io/en/stable/api/generated/scanpy.pl.pca_loadings.html>`__
 
 PCA: Plot the variance ratio (`pl.pca_variance_ratio`)
 ======================================================
 
 More details on the `scanpy documentation
-<https://icb-scanpy.readthedocs-hosted.com/en/stable/api/scanpy.pl.pca_variance_ratio.html>`__
+<https://scanpy.readthedocs.io/en/stable/api/generated/scanpy.pl.pca_variance_ratio.html>`__
 
 PCA: Plot PCA results (`pl.pca_overview`)
 =========================================
@@ -2364,37 +2364,37 @@
 if you want to change the default settings.
 
 More details on the `scanpy documentation
-<https://icb-scanpy.readthedocs-hosted.com/en/stable/api/scanpy.pl.pca_overview.html>`__
+<https://scanpy.readthedocs.io/en/stable/api/generated/scanpy.pl.pca_overview.html>`__
 
 Embedding: Scatter plot in tSNE basis (`pl.tsne`)
 =================================================
 
 More details on the `scanpy documentation
-<https://icb-scanpy.readthedocs-hosted.com/en/stable/api/scanpy.pl.tsne.html>`__
+<https://scanpy.readthedocs.io/en/stable/api/generated/scanpy.pl.tsne.html>`__
 
 Embeddings: Scatter plot in UMAP basis (`pl.umap`)
 ==================================================
 
 More details on the `scanpy documentation
-<https://icb-scanpy.readthedocs-hosted.com/en/stable/api/scanpy.pl.umap.html>`__
+<https://scanpy.readthedocs.io/en/stable/api/generated/scanpy.pl.umap.html>`__
 
 Embeddings: Scatter plot in Diffusion Map basis (`pl.diffmap`)
 ==============================================================
 
 More details on the `scanpy documentation
-<https://icb-scanpy.readthedocs-hosted.com/en/stable/api/scanpy.pl.diffmap.html>`__
+<https://scanpy.readthedocs.io/en/stable/api/generated/scanpy.pl.diffmap.html>`__
 
 Branching trajectories and pseudotime, clustering: Plot groups and pseudotime (`pl.dpt_groups_pseudotime`)
 ===========================================================================================================
 
 More details on the `scanpy documentation
-<https://icb-scanpy.readthedocs-hosted.com/en/stable/api/scanpy.pl.dpt_groups_pseudotime.html>`__
+<https://scanpy.readthedocs.io/en/stable/api/generated/scanpy.pl.dpt_groups_pseudotime.html>`__
 
 Branching trajectories and pseudotime, clustering: Heatmap of pseudotime series (`pl.dpt_timeseries`)
 =====================================================================================================
 
 More details on the `scanpy documentation
-<https://icb-scanpy.readthedocs-hosted.com/en/stable/api/scanpy.pl.dpt_timeseries.html>`__
+<https://scanpy.readthedocs.io/en/stable/api/generated/scanpy.pl.dpt_timeseries.html>`__
 
 
 Branching trajectories and pseudotime, clustering: Plot the abstracted graph through thresholding low-connectivity edges (`pl.paga`)
@@ -2407,56 +2407,56 @@
 `maxiter` parameter by 1 if the layout is flipped.
 
 More details on the `scanpy documentation
-<https://icb-scanpy.readthedocs-hosted.com/en/stable/api/scanpy.pl.paga.html>`__
+<https://scanpy.readthedocs.io/en/stable/api/generated/scanpy.pl.paga.html>`__
 
 
 Branching trajectories and pseudotime, clustering: Scatter and PAGA graph side-by-side (`pl.paga_compare`)
 ==========================================================================================================
 
 More details on the `scanpy documentation
-<https://icb-scanpy.readthedocs-hosted.com/en/stable/api/scanpy.pl.paga_compare.html>`__
+<https://scanpy.readthedocs.io/en/stable/api/generated/scanpy.pl.paga_compare.html>`__
 
 Branching trajectories and pseudotime, clustering: Gene expression and annotation changes along paths (`pl.paga_path`)
 ======================================================================================================================
 
 More details on the `scanpy documentation
-<https://icb-scanpy.readthedocs-hosted.com/en/stable/api/scanpy.pl.paga_path.html>`__
+<https://scanpy.readthedocs.io/en/stable/api/generated/scanpy.pl.paga_path.html>`__
 
 Marker genes: Plot ranking of genes using dotplot plot (`pl.rank_genes_groups`)
 ===============================================================================
 
 More details on the `scanpy documentation
-<https://icb-scanpy.readthedocs-hosted.com/en/stable/api/scanpy.pl.rank_genes_groups.html>`__
+<https://scanpy.readthedocs.io/en/stable/api/generated/scanpy.pl.rank_genes_groups.html>`__
 
 Marker genes: Plot ranking of genes as violin plot (`pl.rank_genes_groups_violin`)
 ==================================================================================
 
 More details on the `scanpy documentation
-<https://icb-scanpy.readthedocs-hosted.com/en/stable/api/scanpy.pl.rank_genes_groups_violin.html>`__
+<https://scanpy.readthedocs.io/en/stable/api/generated/scanpy.pl.rank_genes_groups_violin.html>`__
 
 Marker genes: Plot ranking of genes as dotplot plot (`pl.rank_genes_groups_dotplot`)
 ====================================================================================
 
 More details on the `scanpy documentation
-<https://icb-scanpy.readthedocs-hosted.com/en/stable/api/scanpy.pl.rank_genes_groups_dotplot.html>`__
+<https://scanpy.readthedocs.io/en/stable/api/generated/scanpy.pl.rank_genes_groups_dotplot.html>`__
 
 Marker genes: Plot ranking of genes as heatmap plot (`pl.rank_genes_groups_heatmap`)
 ====================================================================================
 
 More details on the `scanpy documentation
-<https://icb-scanpy.readthedocs-hosted.com/en/stable/api/scanpy.pl.rank_genes_groups_heatmap.html>`__
+<https://scanpy.readthedocs.io/en/stable/api/generated/scanpy.pl.rank_genes_groups_heatmap.html>`__
 
 Marker genes: Plot ranking of genes as matrixplot plot (`pl.rank_genes_groups_matrixplot`)
 ==========================================================================================
 
 More details on the `scanpy documentation
-<https://icb-scanpy.readthedocs-hosted.com/en/stable/api/scanpy.pl.rank_genes_groups_matrixplot.html>`__
+<https://scanpy.readthedocs.io/en/stable/api/generated/scanpy.pl.rank_genes_groups_matrixplot.html>`__
 
 Marker genes: Plot ranking of genes as stacked violin plot (`pl.rank_genes_groups_stacked_violin`)
 ==================================================================================================
 
 More details on the `scanpy documentation
-<https://icb-scanpy.readthedocs-hosted.com/en/stable/api/scanpy.pl.rank_genes_groups_stacked_violin.html>`__
+<https://scanpy.readthedocs.io/en/stable/api/generated/scanpy.pl.rank_genes_groups_stacked_violin.html>`__
     ]]></help>
     <expand macro="citations"/>
 </tool>