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getPatternGeneSet: replace pathways column with gene.set #108

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May 29, 2024
Merged

getPatternGeneSet: replace pathways column with gene.set #108

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70f4078
replace pathway column with gene.set
jmitchell81 May 29, 2024
416bd54
test significant gene sets
jmitchell81 May 29, 2024
41826c7
bump version
dimalvovs May 29, 2024
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2 changes: 1 addition & 1 deletion DESCRIPTION
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Original file line number Diff line number Diff line change
@@ -1,5 +1,5 @@
Package: CoGAPS
Version: 3.24.0
Version: 3.24.1
Date: 2024-03-22
Title: Coordinated Gene Activity in Pattern Sets
Author: Jeanette Johnson, Ashley Tsang, Jacob Mitchell, Thomas Sherman, Wai-shing Lee, Conor Kelton, Ondrej Maxian, Jacob Carey,
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8 changes: 4 additions & 4 deletions R/methods-CogapsResult.R
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Expand Up @@ -311,10 +311,10 @@ function(object, gene.sets, method = c("enrichment", "overrepresentation"), ...)
amp <- A[,p]
names(amp) <- features
result <- fgsea::fgsea(pathways = gene.sets, stats = amp, scoreType = "pos")
result <- dplyr::rename(result, gene.set = "pathway")
result <- dplyr::mutate(result,gene.set=forcats::fct_reorder(gene.set, - padj))
result$leadingEdge <- vapply(result$leadingEdge, FUN = toString, FUN.VALUE = character(1))
result$neg.log.padj <- (-10) * log10(result$padj)
result$gene.set <- names(gene.sets)
result <- dplyr::mutate(result,gene.set=forcats::fct_reorder(gene.set, - padj))
return(result)
}
)
Expand All @@ -332,10 +332,10 @@ function(object, gene.sets, method = c("enrichment", "overrepresentation"), ...)
pathways = gene.sets, genes = PMlist[[p]],
universe = features,
maxSize=2038)
result <- dplyr::rename(result, gene.set = "pathway")
result <- dplyr::mutate(result,gene.set=forcats::fct_reorder(gene.set, - padj))
result[["k/K"]] <- result$overlap / result$size
result$neg.log.padj <- (-10) * log10(result$padj)
result$gene.set <- names(gene.sets)
result <- dplyr::mutate(result,gene.set=forcats::fct_reorder(gene.set, - padj))
return(result)
}
)
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12 changes: 12 additions & 0 deletions tests/testthat/test_getPatternGeneSet.R
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thank you for adding tests!

Original file line number Diff line number Diff line change
Expand Up @@ -2,6 +2,7 @@ test_that("getPatternGeneSet works on enrichment test", {
#set up
data(GIST)
gs.test <- list(
"sig_p1" = c("Hs.479754", "Hs.491582", "Hs.155591", "Hs.443625", "Hs.170355","Hs.191911"),
"gs1" = c("Hs.2", "Hs.4", "Hs.36", "Hs.96", "Hs.202"),
"gs2" = c("Hs.699463", "Hs.699288", "Hs.699280", "Hs.699154", "Hs.697294")
)
Expand All @@ -12,6 +13,7 @@ test_that("getPatternGeneSet works on overrepresentation test", {
#set up
data(GIST)
gs.test <- list(
"sig_p1" = c("Hs.479754", "Hs.491582", "Hs.155591", "Hs.443625", "Hs.170355","Hs.191911"),
"gs1" = c("Hs.2", "Hs.4", "Hs.36", "Hs.96", "Hs.202"),
"gs2" = c("Hs.699463", "Hs.699288", "Hs.699280", "Hs.699154", "Hs.697294")
)
Expand All @@ -22,10 +24,15 @@ test_that("plotPatternGeneSet renders a plot for enrichment test", {
#set up
data(GIST)
gs.test <- list(
"sig_p1" = c("Hs.479754", "Hs.491582", "Hs.155591", "Hs.443625", "Hs.170355","Hs.191911"),
"gs1" = c("Hs.2", "Hs.4", "Hs.36", "Hs.96", "Hs.202"),
"gs2" = c("Hs.699463", "Hs.699288", "Hs.699280", "Hs.699154", "Hs.697294")
)
gpgs_res <- getPatternGeneSet(object = GIST.result, gene.sets = gs.test, method = "enrichment")
significant_result <- gpgs_res[[1]][gpgs_res[[1]]$gene.set == "sig_p1",]

expect_true(significant_result$padj < 0.05)

pl <- plotPatternGeneSet(patterngeneset = gpgs_res, whichpattern = 1, padj_threshold = 1)

expect_is(pl$layers[[1]], "ggproto")
Expand All @@ -36,10 +43,15 @@ test_that("plotPatternGeneSet renders a plot for overrepresentation test", {
#set up
data(GIST)
gs.test <- list(
"sig_p1" = c("Hs.479754", "Hs.491582", "Hs.155591", "Hs.443625", "Hs.170355","Hs.191911"),
"gs1" = c("Hs.2", "Hs.4", "Hs.36", "Hs.96", "Hs.202"),
"gs2" = c("Hs.699463", "Hs.699288", "Hs.699280", "Hs.699154", "Hs.697294")
)
gpgs_res <- getPatternGeneSet(object = GIST.result, gene.sets = gs.test, method = "overrepresentation", threshold = "cut")
significant_result <- gpgs_res[[1]][gpgs_res[[1]]$gene.set == "sig_p1",]

expect_true(significant_result$padj < 0.05)

pl <- plotPatternGeneSet(patterngeneset = gpgs_res, whichpattern = 1, padj_threshold = 1)

expect_is(pl$layers[[1]], "ggproto")
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