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Merged
immanuelazn merged 3 commits into from
Nov 26, 2024
Merged

Ia/fix lapply plot bug #2240

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44e5a31
test plotting lapply
immanuelazn Nov 26, 2024
cbb201b
fix suppresswarnings typo
immanuelazn Nov 26, 2024
15d4270
fix legend plotting lapply on R<4.3
immanuelazn Nov 26, 2024
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2 changes: 1 addition & 1 deletion R/RNAIntegration.R
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Original file line number Diff line number Diff line change
Expand Up @@ -478,7 +478,7 @@ addGeneIntegrationMatrix <- function(
colnames(mat) <- as.character(colnames(mat))
#Log-Normalize
mat <- log(mat + 1) #use natural log
seuratATAC <- supressWarninggs(Seurat::CreateSeuratObject(counts = as.matrix(mat[head(seq_len(nrow(mat)), 5), , drop = FALSE])))
seuratATAC <- suppressWarnings(Seurat::CreateSeuratObject(counts = as.matrix(mat[head(seq_len(nrow(mat)), 5), , drop = FALSE])))
seuratATAC[["GeneScore"]] <- Seurat::CreateAssayObject(counts = mat)

#Clean Memory
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7 changes: 5 additions & 2 deletions R/VisualizeData.R
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Expand Up @@ -882,11 +882,14 @@ plotGroups <- function(

#adapted from https://github.com/jwdink/egg/blob/master/R/set_panel_size.r
g <- ggplotGrob(p)

legend_indices <- grep("guide-box", g$layout$name)
# ggplot versions > 3.5 can have multiple guide boxes, and are non automatically removed if is a "zeroGrob"
# Do filtering wrt only non "zeroGrob" legends
legend <- legend_indices[sapply(legend_indices, function(idx) class(g$grobs[[idx]])[1] != "zeroGrob")]
if (length(legend_indices) != 0) {
legend <- legend_indices[unlist(lapply(legend_indices, function(idx) class(g$grobs[[idx]])[1] != "zeroGrob"))]
} else {
legend <- legend_indices
}
# add correct ones to legend
if(length(legend)!=0){
gl <- g$grobs[[legend]]
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