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Lint R scripts

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This commit is contained in:
Bryan Roessler
2024-08-13 15:59:18 -04:00
parent f190967383
commit 79862ddab4
4 changed files with 185 additions and 170 deletions
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14
workflow/apps/r/createHeatMaps.R
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@@ -171,7 +171,7 @@ for (i in 1:num_unique_clusts) {
if (cluster_length != 1) {
X0 <- as.matrix(cluster_data[, 4:(length(hmapfile[1, ]) - 2)])
if (cluster_length >= 2001) {
mypath <- file.path(outDir, paste("cluster_", gsub(" ", "", cluster), sep = ""), ".pdf")
mypath <- file.path(outDir, paste("cluster_", gsub(" ", "", cluster), ".pdf", sep = ""))
pdf(file = mypath, height = 20, width = 15)
heatmap.2(
x = X0,
@@ -191,7 +191,7 @@ for (i in 1:num_unique_clusts) {
dev.off()
}
if (cluster_length >= 201 && cluster_length <= 2000) {
mypath <- file.path(outDir, paste("cluster_", gsub(" ", "", cluster), sep = ""), ".pdf")
mypath <- file.path(outDir, paste("cluster_", gsub(" ", "", cluster), ".pdf", sep = ""))
pdf(file = mypath, height = 15, width = 12)
heatmap.2(
x = X0,
@@ -210,7 +210,7 @@ for (i in 1:num_unique_clusts) {
dev.off()
}
if (cluster_length >= 150 && cluster_length <= 200) {
mypath <- file.path(outDir, paste("cluster_", gsub(" ", "", cluster), sep = ""), ".pdf")
mypath <- file.path(outDir, paste("cluster_", gsub(" ", "", cluster), ".pdf", sep = ""))
pdf(file = mypath, height = 12, width = 12)
heatmap.2(
x = X0,
@@ -228,7 +228,7 @@ for (i in 1:num_unique_clusts) {
dev.off()
}
if (cluster_length >= 101 && cluster_length <= 149) {
mypath <- file.path(outDir, paste("cluster_", gsub(" ", "", cluster), sep = ""), ".pdf")
mypath <- file.path(outDir, paste("cluster_", gsub(" ", "", cluster), ".pdf", sep = ""))
pdf(file = mypath, mypath, height = 12, width = 12)
heatmap.2(
x = X0,
@@ -246,7 +246,7 @@ for (i in 1:num_unique_clusts) {
dev.off()
}
if (cluster_length >= 60 && cluster_length <= 100) {
mypath <- file.path(outDir, paste("cluster_", gsub(" ", "", cluster), sep = ""), ".pdf")
mypath <- file.path(outDir, paste("cluster_", gsub(" ", "", cluster), ".pdf", sep = ""))
pdf(file = mypath, height = 12, width = 12)
heatmap.2(
x = X0,
@@ -264,7 +264,7 @@ for (i in 1:num_unique_clusts) {
dev.off()
}
if (cluster_length <= 59 && cluster_length >= 30) {
mypath <- file.path(outDir, paste("cluster_", gsub(" ", "", cluster), sep = ""), ".pdf")
mypath <- file.path(outDir, paste("cluster_", gsub(" ", "", cluster), ".pdf", sep = ""))
pdf(file = mypath, height = 9, width = 12)
heatmap.2(
x = X0,
@@ -282,7 +282,7 @@ for (i in 1:num_unique_clusts) {
dev.off()
}
if (cluster_length <= 29) {
mypath <- file.path(outDir, paste("cluster_", gsub(" ", "", cluster), sep = ""), ".pdf")
mypath <- file.path(outDir, paste("cluster_", gsub(" ", "", cluster), ".pdf", sep = ""))
pdf(file = mypath, height = 7, width = 12)
heatmap.2(
x = X0,