# HG changeset patch
# User iuc
# Date 1726317860 0
# Node ID 2dfb2227a16c9f212a6f4b66d7c6c3a1ab0fb1c8
# Parent 1072ce66b426ae76edef7bb2e10b20d05dc97158
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
diff -r 1072ce66b426 -r 2dfb2227a16c README.md
--- a/README.md Tue Aug 20 09:53:51 2024 +0000
+++ b/README.md Sat Sep 14 12:44:20 2024 +0000
@@ -25,6 +25,7 @@
`pp.highly_variable_genes` | Extract highly variable genes
`pp.subsample` | Subsample to a fraction of the number of observations
`pp.downsample_counts` | Downsample counts so that each cell has no more than target_counts
+ `pp.scrublet` | Predict doublets
3. Normalize (`normalize.xml`)
@@ -34,14 +35,18 @@
`pp.recipe_zheng17` | Normalization and filtering as of [Zheng17]
`pp.recipe_weinreb17` | Normalization and filtering as of [Weinreb17]
`pp.recipe_seurat` | Normalization and filtering as of Seurat [Satija15]
+ `external.pp.magic` | Denoising using Markov Affinity-based Graph Imputation of Cells (MAGIC) API
4. Remove confounders (`remove_confounder.xml`)
Methods | Description
--- | ---
`pp.regress_out` | Regress out unwanted sources of variation
- `pp.mnn_correct` | Correct batch effects by matching mutual nearest neighbors
+
`pp.combat` | ComBat function for batch effect correction
+ `external.pp.bbknn` | Batch effect removal with Batch balanced KNN (BBKNN)
+ `external.pp.harmony_integrate` | Integrate multiple single-cell experiments with Harmony
+ `external.pp.scanorama_integrate` | Integrate multiple single-cell experiments with Scanorama
5. Clustering, embedding and trajectory inference (`cluster_reduce_dimension.xml`)
@@ -49,14 +54,14 @@
--- | ---
`tl.louvain` | Cluster cells into subgroups
`tl.leiden` | Cluster cells into subgroups
- `tl.pca` | Principal component analysis
- `pp.pca` | Principal component analysis (appears to be the same func...)
+ `pp.pca` | Principal component analysis
`tl.diffmap` | Diffusion Maps
`tl.tsne` | t-SNE
`tl.umap` | Embed the neighborhood graph using UMAP
`tl.draw_graph` | Force-directed graph drawing
`tl.dpt` | Infer progression of cells through geodesic distance along the graph
`tl.paga` | Mapping out the coarse-grained connectivity structures of complex manifolds
+ `tl.embedding_density` | Calculate the density of cells in an embedding (per condition)
6. Plot (`plot.xml`)
@@ -66,18 +71,20 @@
--- | ---
`pl.scatter` | Scatter plot along observations or variables axes
`pl.heatmap` | Heatmap of the expression values of set of genes
+ `pl.tracksplot` | Tracks plot of the expression values per cell
`pl.dotplot` | Makes a dot plot of the expression values
`pl.violin` | Violin plot
`pl.stacked_violin` | Stacked violin plots
`pl.matrixplot` | Heatmap of the mean expression values per cluster
`pl.clustermap` | Hierarchically-clustered heatmap
-
+
2. Preprocessing
Methods | Description
--- | ---
`pl.highest_expr_genes` | Plot the fraction of counts assigned to each gene over all cells
`pl.highly_variable_genes` | Plot dispersions versus means for genes
+ `pl.scrublet_score_distribution` | Histogram of doublet scores
3. PCA
@@ -96,12 +103,13 @@
`pl.umap` | Scatter plot in UMAP basis
`pl.diffmap` | Scatter plot in Diffusion Map basis
`pl.draw_graph` | Scatter plot in graph-drawing basis
+ `pl.embedding_density` | Density of cells in an embedding (per condition)
5. Branching trajectories and pseudotime, clustering
Methods | Description
--- | ---
- `pl.dpt_groups_pseudotime` | Plot groups and pseudotime
+
`pl.dpt_timeseries` | Heatmap of pseudotime series
`pl.paga` | Plot the abstracted graph through thresholding low-connectivity edges
`pl.paga_compare` | Scatter and PAGA graph side-by-side
@@ -113,3 +121,8 @@
--- | ---
`pl.rank_genes_groups` | Plot ranking of genes using dotplot plot
`pl.rank_genes_groups_violin` | Plot ranking of genes for all tested comparisons
+ `pl.rank_genes_groups_stacked_violin` | Plot ranking of genes as stacked violin plot
+ `pl.rank_genes_groups_heatmap` | Plot ranking of genes as heatmap plot
+ `pl.rank_genes_groups_dotplot` | Plot ranking of genes as dotplot plot
+ `pl.rank_genes_groups_matrixplot` | Plot ranking of genes as matrixplot plot
+ `pl.rank_genes_groups_tracksplot` | Plot ranking of genes as tracksplot plot
diff -r 1072ce66b426 -r 2dfb2227a16c macros.xml
--- a/macros.xml Tue Aug 20 09:53:51 2024 +0000
+++ b/macros.xml Sat Sep 14 12:44:20 2024 +0000
@@ -1,17 +1,15 @@
- 1.9.6
- 4
- 21.09
+ 1.10.2
+ 0
+ 21.09
scanpy
- loompy
- leidenalg
- louvain
- pandas
- matplotlib
- seaborn
- magic-impute
+ anndata
+ numpy
+ pandas
+ scipy
+ statsmodels
@@ -22,7 +20,7 @@
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@@ -31,28 +29,13 @@
10.1093/gigascience/giaa102
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- '$hidden_output' &&
-python '$script_file' >> '$hidden_output' &&
-ls . >> '$hidden_output' &&
-touch 'anndata_info.txt' &&
-cat 'anndata_info.txt' @CMD_prettify_stdout@
- ]]>
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- #set $var_group_labels=[]
- #for $i, $s in enumerate($method.var_group_positions)
- #silent $var_group_positions.append((int($s.start), int($s.end)))
- #silent $var_group_labels.append(str($s.label))
- #end for
- var_group_positions=$var_group_positions,
- var_group_labels=$var_group_labels,
- #end if
- #if str($method.var_group_rotation) != ''
- var_group_rotation=$method.var_group_rotation,
- #end if
- #if $method.figsize.test == 'yes'
- figsize=($method.figsize.width, $method.figsize.height),
- #end if
- #if $method.layer
- layer='$method.layer',
- #end if
- ]]>
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+ '$hidden_output' &&
+python '$script_file' >> '$hidden_output' &&
+ls . >> '$hidden_output' &&
+touch 'anndata_info.txt' &&
+cat 'anndata_info.txt' @CMD_PRETTIFY_STDOUT@
+ ]]>
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- #end for
- components=$components,
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+ #set $var_group_positions=[]
+ #set $var_group_labels=[]
+ #for $i, $s in enumerate($method.var_group_positions)
+ #silent $var_group_positions.append((int($s.start), int($s.end)))
+ #silent $var_group_labels.append(str($s.label))
+ #end for
+ var_group_positions=$var_group_positions,
+ var_group_labels=$var_group_labels,
#end if
- #if str($method.dot_max) != ''
- dot_max=$method.dot_max,
+ #if str($method.var_group_rotation) != '':
+ var_group_rotation=$method.var_group_rotation,
#end if
- #if str($method.dot_min) != ''
- dot_min=$method.dot_min,
- #end if
- @CMD_params_matplotlib_pyplot_scatter@
+ @CMD_PARAMS_FIGSIZE@
+ @CMD_PARAM_LAYER@
]]>
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+ #set $components=[]
+ #for $i, $s in enumerate($method.plot.components)
+ #silent $components.append(str($s.axis1) + ',' + str($s.axis2))
+ #end for
+ components=$components,
+#end if
+ ]]>
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diff -r 1072ce66b426 -r 2dfb2227a16c plot.xml
--- a/plot.xml Tue Aug 20 09:53:51 2024 +0000
+++ b/plot.xml Sat Sep 14 12:44:20 2024 +0000
@@ -1,10 +1,13 @@
-
- with scanpy
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macros.xml
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+ matplotlib
+ seaborn
+ python-igraph
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-
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+
`__
+Generic: Tracks plot (`pl.tracksplot`)
+======================================
+
+In this type of plot each var_name is plotted as a filled line plot where the y values correspond to the var_name values and x is each of the cells.
+Best results are obtained when using raw counts that are not log.
+
+More details on the `scanpy documentation
+`__
+
Generic: Violin plot (`pl.violin`)
==================================
@@ -2438,6 +2313,15 @@
More details on the `scanpy documentation
`__
+Preprocessing: Plot histogram of doublet scores for observed transcriptomes and simulated doublets (`pl.scrublet_score_distribution`)
+=====================================================================================================================================
+
+The histogram for simulated doublets is useful for determining the correct doublet score threshold.
+Scrublet must have been run previously with the input object.
+
+More details on the `scanpy documentation
+`__
+
PCA: Scatter plot in PCA coordinates (`pl.pca`)
===============================================
@@ -2483,11 +2367,24 @@
More details on the `scanpy documentation
`__
-Branching trajectories and pseudotime, clustering: Plot groups and pseudotime (`pl.dpt_groups_pseudotime`)
-===========================================================================================================
+Embeddings: Scatter plot in graph-drawing basis (`pl.draw_graph`)
+=================================================================
More details on the `scanpy documentation
-`__
+`__
+
+Embeddings: Plot the density of cells in an embedding (per condition) (`pl.embedding_density`)
+==============================================================================================
+
+More details on the `scanpy documentation
+`__
+
+.. This function is commented out because it is not compatible with pandas version. If the issue is not resolved in the next update, this should be removed.
+.. Branching trajectories and pseudotime, clustering: Plot groups and pseudotime (`pl.dpt_groups_pseudotime`)
+.. ===========================================================================================================
+
+.. More details on the `scanpy documentation
+.. `__
Branching trajectories and pseudotime, clustering: Heatmap of pseudotime series (`pl.dpt_timeseries`)
=====================================================================================================
@@ -2533,11 +2430,11 @@
More details on the `scanpy documentation
`__
-Marker genes: Plot ranking of genes as dotplot plot (`pl.rank_genes_groups_dotplot`)
-====================================================================================
+Marker genes: Plot ranking of genes as stacked violin plot (`pl.rank_genes_groups_stacked_violin`)
+==================================================================================================
More details on the `scanpy documentation
-`__
+`__
Marker genes: Plot ranking of genes as heatmap plot (`pl.rank_genes_groups_heatmap`)
====================================================================================
@@ -2545,17 +2442,19 @@
More details on the `scanpy documentation
`__
+Marker genes: Plot ranking of genes as dotplot plot (`pl.rank_genes_groups_dotplot`)
+====================================================================================
+
+More details on the `scanpy documentation
+`__
+
Marker genes: Plot ranking of genes as matrixplot plot (`pl.rank_genes_groups_matrixplot`)
==========================================================================================
More details on the `scanpy documentation
`__
-Marker genes: Plot ranking of genes as stacked violin plot (`pl.rank_genes_groups_stacked_violin`)
-==================================================================================================
-
-More details on the `scanpy documentation
-`__
- ]]>
+ ]]>
+
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