Add ImageDimPlot, ImageFeaturePlot to Seurat Visualize #7501

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 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

View reviewed changes

nilchia requested a review from Copilot December 3, 2025 15:36

Copilot started reviewing on behalf of nilchia December 3, 2025 15:37 View session

Copilot finished reviewing on behalf of nilchia December 3, 2025 15:41

Copilot AI 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

View reviewed changes

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

Merged

	<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)"/>

Add ImageDimPlot, ImageFeaturePlot to Seurat Visualize #7501

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khaled196 commented Dec 2, 2025 •

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