Adding new method: scMerge2 by seohyonkim · Pull Request #63 · openproblems-bio/task_batch_integration

seohyonkim · 2025-06-04T20:47:04Z

Describe your changes

This PR is for a new method scMerge2.

Checklist before requesting a review

I have performed a self-review of my code
Check the correct box. Does this PR contain:
- Breaking changes
- New functionality
- Major changes
- Minor changes
- Bug fixes
Proposed changes are described in the CHANGELOG.md
CI Tests succeed and look good!

seohyonkim · 2025-07-23T13:58:54Z

@lazappi Hi! This is Seo :)
The previously-working version of this method is failing now, could you please see why? Is there anything new that has changed?
Thank you so much!

src/methods/semisupervised_scmerge2/config.vsh.yaml

Co-authored-by: Luke Zappia <lazappi@users.noreply.github.com>

rcannood · 2025-08-08T14:34:04Z

@mumichae Could you take a look at this PR?

src/methods/semisupervised_scmerge2/script.R

src/methods/semisupervised_scmerge2/config.vsh.yaml

src/methods/unsupervised_scmerge2/script.R

seohyonkim · 2025-09-08T23:24:55Z

@mumichae I fixed up the code with the help of your feedback!
Here are some key points to help you review the code quicker (and also to help myself):

scMerge2 takes and returns the matrix of gene x cell, not cell x gene, so I transpose the matrix in the beginning and before storing it to the output
top_n for the SEG selection is set for 1000 by default, but for small test data, I did min(top_n, nrow(seg_df)) for safety
I did couple of lines such as rownames(counts) <- as.character(adata$var_names) since I'm scared of AnnData conversion dropping them
newY is the return format(?) of scMerge2

Let me know if there are any thing else that can be better :)

mumichae

Already looking a lot better!
There are still some computational bottlenecks that are worth solving (given that this methods uses the complete count matrix and densifying is expensive.

mumichae · 2025-09-25T09:16:02Z

src/methods/unsupervised_scmerge2/script.R

+adata <- anndata::read_h5ad(par$input)
+
+anndataToUnsupervisedScMerge2 <- function(adata, top_n = 1000, verbose = TRUE) {
+  counts <- t(as.matrix(adata$layers[["counts"]]))


Could you preserve the sparsity of the data? According to the documentation, scMerge should be able to deal with sparse matrices. If the matrix is already a dgeMatrix, you can avoid conversion

mumichae · 2025-09-25T09:21:10Z

src/methods/unsupervised_scmerge2/script.R

+
+cat("Run unsupervised scMerge2\n")
+
+scMerge2_res <- anndataToUnsupervisedScMerge2(adata, top_n = 1000L, verbose = TRUE)


Could you make top_n for the control genes a parameter that can be adjusted in the config.vsh.yaml?

mumichae · 2025-09-25T09:24:10Z

src/methods/unsupervised_scmerge2/script.R

+  batch     <- as.character(adata$obs$batch)
+  cellTypes <- as.character(adata$obs$cell_type)
+
+  scMerge2_res <- scMerge2(
+    exprsMat = exprsMat,
+    batch = batch,
+    ctl = ctl,
+    verbose = verbose
+  )


You can simplify the code a bit

Suggested change

batch <- as.character(adata$obs$batch)

cellTypes <- as.character(adata$obs$cell_type)

scMerge2_res <- scMerge2(

exprsMat = exprsMat,

batch = batch,

ctl = ctl,

verbose = verbose

)

scMerge2_res <- scMerge2(

exprsMat = exprsMat,

batch = as.character(adata$obs$batch),

ctl = ctl,

verbose = verbose

)

mumichae · 2025-09-25T09:24:42Z

src/methods/unsupervised_scmerge2/script.R

+  seg_df <- seg_df[order(seg_df$segIdx, decreasing = TRUE), , drop = FALSE]
+  ctl <- rownames(seg_df)[seq_len(min(top_n, nrow(seg_df)))]
+
+  exprsMat <- t(as.matrix(adata$layers[["normalized"]]))


Is densification via as.matrix really necessary here?

mumichae · 2025-09-25T09:26:21Z

src/methods/unsupervised_scmerge2/script.R

+embedding <- prcomp(t(corrected_mat))$x[, 1:10, drop = FALSE]
+rownames(embedding) <- colnames(corrected_mat)


PCA computation is not necessary for feature methods, because the "embedding" will be computed after the integration in a post-processing step. See Combat for example

Suggested change

embedding <- prcomp(t(corrected_mat))$x[, 1:10, drop = FALSE]

rownames(embedding) <- colnames(corrected_mat)

mumichae · 2025-09-25T09:26:39Z

src/methods/unsupervised_scmerge2/script.R

+  obsm = list(
+    X_emb = embedding[as.character(adata$obs_names), , drop = FALSE]  # match input cells
+  ),


PCA not needed here

Suggested change

obsm = list(

X_emb = embedding[as.character(adata$obs_names), , drop = FALSE] # match input cells

),

mumichae · 2025-09-25T09:27:35Z

src/methods/semisupervised_scmerge2/script.R

+  batch     <- as.character(adata$obs$batch)
+  cellTypes <- as.character(adata$obs$cell_type)
+
+  scMerge2_res <- scMerge2(
+    exprsMat = exprsMat,
+    batch = batch,
+    cellTypes = cellTypes,
+    ctl = ctl,
+    verbose = verbose
+  )


Nitpick: simplify code

Suggested change

batch <- as.character(adata$obs$batch)

cellTypes <- as.character(adata$obs$cell_type)

scMerge2_res <- scMerge2(

exprsMat = exprsMat,

batch = batch,

cellTypes = cellTypes,

ctl = ctl,

verbose = verbose

)

scMerge2_res <- scMerge2(

exprsMat = exprsMat,

batch = as.character(adata$obs$batch),

cellTypes = as.character(adata$obs$cell_type),

ctl = ctl,

verbose = verbose

)

mumichae · 2025-09-25T09:28:00Z

src/methods/semisupervised_scmerge2/script.R

Comments from unsupervised scMerge2 apply here as well

mumichae · 2025-09-25T09:28:38Z

src/methods/unsupervised_scmerge2/script.R

+  rownames(counts) <- as.character(adata$var_names)
+  colnames(counts) <- as.character(adata$obs_names)
+
+  seg_df <- scSEGIndex(exprs_mat = counts)


add a comment to document what you are doing here

working unsupervised scmerge2. Need to clear out the comments

3e5c8b9

seohyonkim marked this pull request as draft June 4, 2025 20:47

seohyonkim added 4 commits June 6, 2025 18:00

raise error for unmatched species

1cd2b42

clean unsupervised scmerge2

68c3b98

working semi-supervised scmerge2

9836495

remove comments

e4a1daa

lazappi reviewed Jul 23, 2025

View reviewed changes

src/methods/semisupervised_scmerge2/config.vsh.yaml Outdated Show resolved Hide resolved

seohyonkim and others added 2 commits July 23, 2025 17:33

Update src/methods/semisupervised_scmerge2/config.vsh.yaml

d5eb2d1

Co-authored-by: Luke Zappia <lazappi@users.noreply.github.com>

change image

26712b6

rcannood requested a review from mumichae August 8, 2025 14:33

mumichae marked this pull request as ready for review August 28, 2025 10:56

This was referenced Aug 28, 2025

Add STACAS as new method component #58

Merged

Add CiLISI as new metric component #57

Merged

mumichae requested changes Aug 28, 2025

View reviewed changes

seohyonkim added 3 commits September 9, 2025 01:07

fixed scMerge2

d0437b9

add method_types to config

423057e

add to changelog

dd6b1ce

Merge branch 'main' into feature/scmerge

2668b92

mumichae requested changes Sep 25, 2025

View reviewed changes


		cat("Run unsupervised scMerge2\n")

		scMerge2_res <- anndataToUnsupervisedScMerge2(adata, top_n = 1000L, verbose = TRUE)

		embedding <- prcomp(t(corrected_mat))$x[, 1:10, drop = FALSE]
		rownames(embedding) <- colnames(corrected_mat)

	obsm = list(
	X_emb = embedding[as.character(adata$obs_names), , drop = FALSE] # match input cells
	),

Conversation

seohyonkim commented Jun 4, 2025

Describe your changes

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seohyonkim commented Jul 23, 2025

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rcannood commented Aug 8, 2025

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seohyonkim commented Sep 8, 2025

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