fix input, close #87

[dimalvovs]

fix input for main.nh, close #87

in addition, harmonize SD outputs, before:
// IMScores: IMScores.rds with row names holding gene names,
// followed by cell_type1_near_cell_typeN columns, values are IMScores
// LRscores: LRscores.rds with row names holding ligand-receptor pair names,
// followed by cell_type1_near_cell_typeN columns, values are LRscores
and
// IMScores: spacemarkers.csv first column is Gene with gene name,
// followed by cell_type1_cell_typeN columns, values are spacemarkers

now:
// IMScores: IMScores.rds with row names holding gene names,
// followed by cell_type1_near_cell_typeN columns, values are IMScores
// LRscores: LRscores.rds with row names holding ligand-receptor pair names,
// followed by cell_type1_near_cell_typeN columns, values are LRscores
and
// IMScores: spacemarkers.rds with row names holding gene names,
// followed by cell_type1_cell_typeN columns, values are spacemarkers

[Copilot]

Pull request overview

This PR fixes input handling for the main Nextflow workflow and harmonizes SpaceMarkers output format from CSV to RDS for consistency with other pipeline outputs.

• Changes spaceMarkers output from CSV to RDS format for consistency
• Updates data structure to use row names for gene identifiers instead of a separate column
• Modernizes Groovy syntax from tuple() to bracket notation

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[Copilot]

Pull request overview

Copilot reviewed 1 out of 1 changed files in this pull request and generated 1 comment.

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[Copilot]

After changing the data format to RDS with genes as rownames (lines 67-69), the data frame no longer contains a "Gene" column. However, the plotIMScores function on line 134 expects the input data frame to have a "Gene" column (see R/utils.R line 156: df$genes <- df$Gene). This will cause the plotting code to fail.

Consider converting rownames back to a "Gene" column before calling plotIMScores, for example:

sm <- readRDS("$spaceMarkers")
sm$Gene <- rownames(sm)
plot_names <- colnames(sm)
plot_names <- plot_names[plot_names != "Gene"]

Suggested change

	sm <- readRDS("$spaceMarkers")
	plot_names <- colnames(sm)
	sm <- readRDS("$spaceMarkers")
	sm$Gene <- rownames(sm)
	plot_names <- colnames(sm)
	plot_names <- plot_names[plot_names != "Gene"]

[atuldeshpande]

Looks good! Do we want a temporary colnames sanity check in hdPipeline.R?

[dimalvovs]

actually I tried integrating in the latest version of the pipeline, and it does not look good:
SD outputs IMscores as Gene and spacemarkers metric

_index
cell_type1_cell_type_2
cell_type1_cell_type_3
...

SD does not output LRscores.

HD outputs IMscores as

_index
cell_interaction
effect_size
gene
n1
n2
p.adj
p.value
statistic

HD outputs LRscores as

_index
celltype0_to_celltype1
celltype0_to_celltype2
...

so IMscores for SD looks similar to LRscores of HD, and IMscores of HD looks unique.

Needs fixing by future gen!