Add ImageDimPlot, ImageFeaturePlot to Seurat Visualize by khaled196 · Pull Request #7501 · galaxyproject/tools-iuc

khaled196 · 2025-12-02T15:58:35Z

FOR CONTRIBUTOR:

I have read the CONTRIBUTING.md document and this tool is appropriate for the tools-iuc repo.
License permits unrestricted use (educational + commercial)
This PR adds a new tool or tool collection
This PR updates an existing tool or tool collection
This PR does something else (explain below)

… seurat Co-authored-by: Ona <no-reply@ona.com>

Co-authored-by: Ona <no-reply@ona.com>

pavanvidem · 2025-12-03T13:20:18Z

tools/seurat/macros.xml

        <param argument="smooth" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="false" label="Smooth the graph"/>
    </xml>
+    <xml name="plot_boundaries">
+     <param argument="boundaries" type="text" optional="true" value="" label="Boundaries" help="A vector of segmentation boundaries per image to plot"/>


can you please give an example of such vector in the help text?

tools/seurat/plot.xml

pavanvidem · 2025-12-03T15:24:55Z

tools/seurat/macros.xml

+     <param argument="boundaries" type="text" optional="true" value="" label="Boundaries" help="A vector of segmentation boundaries per image to plot"/>
+    </xml>
+    <xml name="plot_molecules">
+     <param argument="molecules" type="text" optional="true" value="" label="Molecules" help="A vector of molecules to plot"/>


also an example vector in the help text

pavanvidem · 2025-12-03T15:25:29Z

tools/seurat/macros.xml

+    </xml>
+    <xml name="plot_molecules">
+     <param argument="molecules" type="text" optional="true" value="" label="Molecules" help="A vector of molecules to plot"/>
+     <param argument="mols_size" type="float" value="0.1" label="Point size for molecules" help="(mols.size)"/>


is there min, max?

No min and max here. It has nmols that work as max, but this is only used for imagedimplot and not for imagefeatureplot, so I can't add it to the macros as one

pavanvidem · 2025-12-03T15:28:13Z

tools/seurat/macros.xml

+    <param name="mols_alpha" type="float" value="1.0" min="0.0" max="1.0" label="Alpha value for molecules" help=""/>
+    </xml>
+    <xml name="plot_nmols">
+    <param name="nmols" type="integer" value="1000" label="Max number of each molecule specified in `molecules` to plot" help=""/>


pavanvidem · 2025-12-03T15:31:00Z

tools/seurat/plot.xml

+    #if $method.plot.cols.cols == 'one'
+    cols = '$method.plot.cols.cols',
+    #else if $method.plot.cols.cols == 'more'
+    cols = c(unlist(strsplit(gsub(" ", "", '$method.plot.cols.cols_more'), ","))),


is there a select param missing in the xml with one and more values?

removed this option and made it a vector, no need to specify

tools/seurat/plot.xml

Copilot

Pull request overview

This pull request adds support for spatial transcriptomics visualization in Seurat by introducing two new plotting functions: ImageDimPlot for visualizing clusters or categorical groupings in a spatial context, and ImageFeaturePlot for visualizing gene expression in a spatial context. The PR also refactors some existing macro definitions to improve code reuse.

Key Changes:

Added ImageDimPlot and ImageFeaturePlot methods with comprehensive parameter support including FOV selection, boundary visualization, molecule overlays, and spatial-specific styling options
Refactored common plot parameters into reusable XML macros (e.g., plot_na_value, plot_cells, plot_boundaries)
Added test cases with test data files for both new visualization methods

Reviewed changes

Copilot reviewed 2 out of 8 changed files in this pull request and generated 5 comments.

File	Description
tools/seurat/plot.xml	Added R code templates for ImageDimPlot and ImageFeaturePlot functions (lines 249-339), added UI conditional sections for both methods (lines 797-865), added two test cases (lines 1322-1357), and wrapped FeaturePlot min/max_cutoff in conditionals (lines 405-410)
tools/seurat/macros.xml	Added 14 new reusable macros for spatial plotting parameters including plot_fov, plot_boundaries, plot_molecules, plot_border, plot_dark_background, plot_crop, plot_overlap, plot_axes, plot_combine, plot_coord_fixed, plot_flip_xy, and refactored plot_na_value and plot_cells into macros
tools/seurat/test-data/imagefeatureplot.png	Added test output PNG file for ImageFeaturePlot validation
tools/seurat/test-data/imagedimplot.png	Added test output PNG file for ImageDimPlot validation

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Copilot · 2025-12-03T15:42:59Z

tools/seurat/macros.xml

+    <xml name="plot_molecules">
+     <param argument="molecules" type="text" optional="true" value="" label="Molecules" help="A vector of molecules to plot"/>
+     <param argument="mols_size" type="float" value="0.1" label="Point size for molecules" help="(mols.size)"/>
+     <param argument="mols_cols" type="text" optional="true" value="" label="Molecules Colores" help="A vector of color for molecules. The 'Set1' palette from RColorBreweris used by default (make sure they vector has the same length as the molecules)"/>


Multiple issues in the help text: "RColorBreweris" should be "RColorBrewer is" (missing space), and "they vector" should be "the vector"

Suggested change

<param argument="mols_cols" type="text" optional="true" value="" label="Molecules Colores" help="A vector of color for molecules. The 'Set1' palette from RColorBreweris used by default (make sure they vector has the same length as the molecules)"/>

<param argument="mols_cols" type="text" optional="true" value="" label="Molecules Colores" help="A vector of color for molecules. The 'Set1' palette from RColorBrewer is used by default (make sure the vector has the same length as the molecules)"/>

Copilot · 2025-12-03T15:42:59Z

tools/seurat/plot.xml

        </test>
+        <test expect_num_outputs="2">
+            <!-- test12: ImageDimPlot PNG -->
+            <param name="seurat_rds" ftype="rds" value="test_seurat_spatial.rds"/>


The seurat_rds parameter is defined twice. The first definition on line 1324 with ftype="rds" value="test_seurat_spatial.rds" should be removed, as the second definition on line 1325 with the location attribute is the correct one.

Suggested change

<param name="seurat_rds" ftype="rds" value="test_seurat_spatial.rds"/>

tools/seurat/plot.xml

tools/seurat/macros.xml

Co-authored-by: Ona <no-reply@ona.com>

pavanvidem · 2025-12-03T21:52:04Z

tools/seurat/macros.xml

+            <requirement type="package">fit-sne</requirement>
+            <requirement type="package">bioconductor-limma</requirement>
+            <requirement type="package">bioconductor-mast</requirement>
+            <requirement type="package">bioconductor-deseq2</requirement>
+            <requirement type="package">r-svglite</requirement>
+            <requirement type="package">r-metap</requirement>
+            <requirement type="package">bioconductor-glmGamPoi</requirement>
+            <requirement type="package">umap-learn</requirement>
+            <requirement type="package">leidenalg</requirement>
+            <requirement type="package">r-harmony</requirement>
+            <requirement type="package">bioconductor-batchelor</requirement>
+            <requirement type="package">numpy</requirement>
+            <requirement type="package">pandas</requirement>


Please use fixed tool versions. Otherwise, it breaks the reproducibility.

I am solving the conda compatibility right now. But my girpod disconnected.

Co-authored-by: Ona <no-reply@ona.com>

khaled196 · 2026-01-22T11:02:53Z

hi @pavanvidem

Is the pull request ready, or are changes still needed?

tools/seurat/plot.xml

pavanvidem · 2026-01-27T09:23:11Z

tools/seurat/macros.xml

        </xrefs>
-      </xml>
+    </xml>
+    <xml name="creators">


@MarisaJL wrote this entire tool suite initially. Her name is missing. Please carefully check the previous contributors and include only them. Otherwise, I am also fine with removing this whole section :)

Author: Alex Ostrovsky 40246333+astrovsky01@users.noreply.github.com
Author: Alexander OSTROVSKY alexanderostrovsky@Chell.local
Author: Bjoern Gruening bjoern.gruening@gmail.com
Author: Björn Grüning bjoern.gruening@gmail.com
Author: Björn Grüning bjoern@gruenings.eu
Author: Khaled196 56037954+khaled196@users.noreply.github.com
Author: Khaled196 khalled.jooma@yahoo.com
Author: Lance Parsons lparsons@princeton.edu
Author: M Bernt m.bernt@ufz.de
Author: Maria Doyle maria.doyle@petermac.org
Author: Matthias Bernt m.bernt@ufz.de
Author: Mehmet Tekman mtekman89@gmail.com
Author: Nicola Soranzo nicola.soranzo@earlham.ac.uk
Author: Pavankumar Videm pavanvidem@gmail.com
Author: khaled196 khalled.jooma@yahoo.com
Author: mvdbeek m.vandenbeek@gmail.com

The GitHub list of computers from the API

Ok, now I understand what is happening :)
There was an older Seurat (v4) tool in this same folder. The current Seurat (v5) tool was initially named seurat_v5. Seurat v4 has been deprecated, and seurat_v5 has since been renamed to seurat. So this is what I get

$ git log 8ae488affa6ce0299999a4164747d8c160bd994e..HEAD --format='%aN <%aE>' -- seurat | sort -u Bjoern Gruening <bjoern.gruening@gmail.com> Khaled196 <56037954+khaled196@users.noreply.github.com> khaled196 <khalled.jooma@yahoo.com> Khaled196 <khalled.jooma@yahoo.com> Matthias Bernt <m.bernt@ufz.de> M Bernt <m.bernt@ufz.de> Pavankumar Videm <pavanvidem@gmail.com>

wait, but this still did not get Marisa's contribution :) Let me check again

I have added it but didn't push the changes yet 😁

This should hopefully get everyone

$ (git log --format='%aN <%aE>' -- seurat_v5; git log 8ae488affa6ce0299999a4164747d8c160bd994e..HEAD --format='%aN <%aE>' -- seurat; ) | sort -u Bjoern Gruening <bjoern.gruening@gmail.com> Björn Grüning <bjoern@gruenings.eu> Khaled196 <56037954+khaled196@users.noreply.github.com> khaled196 <khalled.jooma@yahoo.com> Khaled196 <khalled.jooma@yahoo.com> MarisaJL <115314387+MarisaJL@users.noreply.github.com> MarisaJL <marisa.loach@open.ac.uk> Matthias Bernt <m.bernt@ufz.de> M Bernt <m.bernt@ufz.de> Pavankumar Videm <pavanvidem@gmail.com>

pavanvidem · 2026-01-27T09:41:06Z

tools/seurat/macros.xml

        <param argument="smooth" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="false" label="Smooth the graph"/>
    </xml>
+    <xml name="plot_boundaries">
+        <param argument="boundaries" type="text" optional="true" value="" label="Boundaries" help="A vector of segmentation boundaries per image to plot e.g boundaries ('slideA_fov1' = 'segmentation', 'slideB_fov2' = 'centroids')"/>


It is hard to expect an input that looks like ('slideA_fov1' = 'segmentation', 'slideB_fov2' = 'centroids') from users. If it requires a dictionary like input, then split this param into a repeat with two params. If a simple comma-separated list of FOVs is good enough, then please adjust the help text.

pavanvidem · 2026-01-27T10:05:59Z

tools/seurat/macros.xml

    </xml>
    <xml name="plot_alpha">
-        <param argument="alpha" type="integer" value="1" label="Alpha value for points"/>
+        <param argument="alpha" type="integer" optional="true" value="1" label="Alpha value for points"/>


pavanvidem · 2026-01-27T10:28:19Z

tools/seurat/create_seurat.xml

                </assert_contents>
            </output>
-            <output name="rds_out" location="https://zenodo.org/records/13732784/files/rawdata.rds" ftype="rds"/>
+            <output name="rds_out" location="https://zenodo.org/records/17817806/files/rawdata.rds" ftype="rds"/>


can you please submit this zenodo record to Galaxy tool-devs community so that the community can maintain the record. If you edit the record, there should be an option to choose the community.

tools/seurat/inspect_and_manipulate.xml

pavanvidem · 2026-01-27T10:41:07Z

tools/seurat/neighbors_clusters_markers.xml

-            <output name="rds_out" location="https://zenodo.org/records/13732784/files/conserved_markers.rds" ftype="rds"/>
-            <output name="markers_tabular" location="https://zenodo.org/records/13732784/files/conserved_markers.csv" ftype="csv">
+            <output name="rds_out" location="https://zenodo.org/records/17817806/files/conserved_markers.rds" ftype="rds"/>
+            <output name="markers_tabular" location="https://zenodo.org/records/17817806/files/conserved_markers.csv" ftype="csv">


with such p-low values in the table, this strict file comparison might break in the future. Please use assert_contents with expression.

pavanvidem · 2026-01-27T10:42:02Z

tools/seurat/neighbors_clusters_markers.xml

-            <output name="rds_out" location="https://zenodo.org/records/13732784/files/markersMAST.rds" ftype="rds"/>
-            <output name="markers_tabular" location="https://zenodo.org/records/13732784/files/markersMAST.csv" ftype="csv">
+            <output name="rds_out" location="https://zenodo.org/records/17817806/files/markersMAST.rds" ftype="rds" compare="sim_size" />
+            <output name="markers_tabular" location="https://zenodo.org/records/17817806/files/markersMAST.csv" ftype="csv" compare="sim_size">


with such p-low values in the table, this strict file comparison might break in the future. Please use assert_contents with expression.

pavanvidem · 2026-01-27T10:42:31Z

tools/seurat/neighbors_clusters_markers.xml

-            <output name="rds_out" location="https://zenodo.org/records/13732784/files/markersDESeq2.rds" ftype="rds"/>
-            <output name="markers_tabular" location="https://zenodo.org/records/13732784/files/markersDESeq2.csv" ftype="csv">
+            <output name="rds_out" location="https://zenodo.org/records/17817806/files/markersDESeq2.rds" ftype="rds" compare="sim_size"/>
+            <output name="markers_tabular" location="https://zenodo.org/records/17817806/files/markersDESeq2.csv" ftype="csv" compare="sim_size">


same here. please use assert_contents

Co-authored-by: Pavankumar Videm <pavanvidem@gmail.com>

khaled196 added 3 commits December 2, 2025 15:52

add ImageDimPlot, ImageFeaturePlot

4066582

add ImageDimPlot, ImageFeaturePlot

a6f5d12

adjost lines

1bfc882

khaled196 requested a review from nsoranzo as a code owner December 2, 2025 15:58

khaled196 marked this pull request as draft December 2, 2025 15:58

khaled196 and others added 6 commits December 2, 2025 18:51

adjost the parameters and fix the cinfig

52b93ce

Merge branch 'galaxyproject:main' into seurat

dbbac01

update plot.xml

59fe0ca

update plot.xml

2de8cc2

Merge branch 'seurat' of https://github.com/bioinfbrad/tools-iuc into…

14900f6

… seurat Co-authored-by: Ona <no-reply@ona.com>

update

1862960

khaled196 marked this pull request as ready for review December 3, 2025 13:23

khaled196 and others added 2 commits December 3, 2025 13:44

adjost the mol_alpha location

3eb93f4

Co-authored-by: Ona <no-reply@ona.com>

fix issues

981b867

pavanvidem reviewed Dec 3, 2025

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khaled196 and others added 3 commits December 3, 2025 16:37

fix indentations

c10112c

Co-authored-by: Ona <no-reply@ona.com>

add help label

105a693

Co-authored-by: Ona <no-reply@ona.com>

add imagedimplot and imagefeatureplot

c2a073d

Co-authored-by: Ona <no-reply@ona.com>

pavanvidem reviewed Dec 3, 2025

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khaled196 and others added 5 commits December 3, 2025 23:13

fix conda hell

8cecec4

Co-authored-by: Ona <no-reply@ona.com>

update seurate version, add creators and update test outptus

6259b27

fix errors

1f3879b

fix identation and add subset_logic

90451a8

Co-authored-by: Ona <no-reply@ona.com>

fix tests

6d295e2

khaled196 requested a review from pavanvidem December 9, 2025 17:42

khaled196 mentioned this pull request Dec 10, 2025

add news about german biohack 2025 galaxyproject/galaxy-hub#3482

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pavanvidem reviewed Jan 27, 2026

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khaled196 and others added 3 commits January 27, 2026 16:13

Update tools/seurat/plot.xml

41daf70

Co-authored-by: Pavankumar Videm <pavanvidem@gmail.com>

Update tools/seurat/inspect_and_manipulate.xml

a76ed4a

Co-authored-by: Pavankumar Videm <pavanvidem@gmail.com>

Update tools/seurat/inspect_and_manipulate.xml

3689897

Co-authored-by: Pavankumar Videm <pavanvidem@gmail.com>

	<param argument="mols_cols" type="text" optional="true" value="" label="Molecules Colores" help="A vector of color for molecules. The 'Set1' palette from RColorBreweris used by default (make sure they vector has the same length as the molecules)"/>
	<param argument="mols_cols" type="text" optional="true" value="" label="Molecules Colores" help="A vector of color for molecules. The 'Set1' palette from RColorBrewer is used by default (make sure the vector has the same length as the molecules)"/>

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khaled196 commented Dec 2, 2025 •

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