# HG changeset patch
# User iuc
# Date 1726317818 0
# Node ID b70219da4a96e6fb5b627d710cbedfb1a581f95b
# Parent a39040ae0a385e2870723d14c24d088d6ab98d7b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
diff -r a39040ae0a38 -r b70219da4a96 README.md
--- a/README.md Tue Aug 20 09:51:42 2024 +0000
+++ b/README.md Sat Sep 14 12:43:38 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 a39040ae0a38 -r b70219da4a96 macros.xml
--- a/macros.xml Tue Aug 20 09:51:42 2024 +0000
+++ b/macros.xml Sat Sep 14 12:43:38 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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advanced_common['show_log']
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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($method.var_group_rotation) != ''
- var_group_rotation=$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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+ density_norm='$method.violin_plot.density_norm',
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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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+ #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 a39040ae0a38 -r b70219da4a96 remove_confounders.xml
--- a/remove_confounders.xml Tue Aug 20 09:51:42 2024 +0000
+++ b/remove_confounders.xml Sat Sep 14 12:43:38 2024 +0000
@@ -1,67 +1,164 @@
-
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with scanpy
macros.xml
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+ bbknn
+ harmonypy
+ scanorama
+ pynndescent
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`__
-Correct batch effects by matching mutual nearest neighbors, using `pp.mnn_correct`
-==================================================================================
+.. This function is commented out because the conda package is not working. Please add this if there is user demand and the conda package is fixed. If not please remove in the next update.
+.. Correct batch effects by matching mutual nearest neighbors, using `external.pp.mnn_correct`
+.. ===========================================================================================
-This uses the implementation of mnnpy. Depending on do_concatenate, it returns AnnData objects in the
-original order containing corrected expression values or a concatenated matrix or AnnData object.
+.. This uses the implementation of mnnpy. Depending on do_concatenate, it returns AnnData objects in the
+.. original order containing corrected expression values or a concatenated matrix or AnnData object.
-Be reminded that it is not advised to use the corrected data matrices for differential expression testing.
+.. Be reminded that it is not advised to use the corrected data matrices for differential expression testing.
-More details on the `scanpy documentation
-`__
+.. More details on the `scanpy documentation
+.. `__
Correct batch effects with ComBat function (`pp.combat`)
@@ -203,6 +531,33 @@
`__
+Correct batch effects with bbknn function (`external.pp.bbknn`)
+===============================================================
+
+Batch balanced kNN alters the kNN procedure to identify each cell’s top neighbours in each batch separately instead of the entire cell pool with no accounting for batch. The nearest neighbours for each batch are then merged to create a final list of neighbours for the cell. Aligns batches in a quick and lightweight manner.
+
+More details on the `scanpy documentation
+`__
+
+
+Correct batch effects with harmony function (`external.pp.harmony_integrate`)
+=============================================================================
+
+Harmony is an algorithm for integrating single-cell data from multiple experiments.
+As Harmony works by adjusting the principal components, this function should be run after performing PCA but before computing the neighbor graph.
+
+More details on the `scanpy documentation
+`__
+
+
+Correct batch effects with scanprama function (`external.pp.scanorama_integrate`)
+=================================================================================
+
+Scanprama is an algorithm for integrating single-cell data from multiple experiments stored in an AnnData object. This function should be run after performing PCA but before computing the neighbor graph.
+
+More details on the `scanpy documentation
+`__
+
]]>
diff -r a39040ae0a38 -r b70219da4a96 test-data/cosg.rank_genes_groups.newton-cg.pbmc68k_highly_reduced_1.h5ad
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diff -r a39040ae0a38 -r b70219da4a96 test-data/pl.clustermap.krumsiek11.png
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diff -r a39040ae0a38 -r b70219da4a96 test-data/pl.dpt_timeseries.dpt.diffmap.neighbors_gauss_braycurtis.recipe_weinreb17.paul15_subsample.png
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diff -r a39040ae0a38 -r b70219da4a96 test-data/pl.embedding_density.pbmc68k_reduced.png
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diff -r a39040ae0a38 -r b70219da4a96 test-data/pl.heatmap.krumsiek11.png
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diff -r a39040ae0a38 -r b70219da4a96 test-data/pl.highest_expr_genes.filter_genes_dispersion.krumsiek11-seurat.png
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diff -r a39040ae0a38 -r b70219da4a96 test-data/pl.highly_variable_genes.seurat.blobs.png
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diff -r a39040ae0a38 -r b70219da4a96 test-data/pl.matrixplot.krumsiek11.png
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diff -r a39040ae0a38 -r b70219da4a96 test-data/pl.paga.paul15_gauss_braycurtis.png
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diff -r a39040ae0a38 -r b70219da4a96 test-data/pl.paga_compare.paul15_gauss_braycurtis.png
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diff -r a39040ae0a38 -r b70219da4a96 test-data/pl.pca.pbmc68k_reduced.CD3D_CD79A_components_2d.pdf
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diff -r a39040ae0a38 -r b70219da4a96 test-data/pl.pca_loadings.pp.pca.krumsiek11.png
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