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Rollup for java clustering

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This commit is contained in:
Bryan Roessler
2024-08-16 17:07:57 -04:00
parent 38b3f66695
commit d1380f9c3b
6032 changed files with 23267 additions and 924 deletions
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30
workflow/apps/r/TSHeatmaps5dev2.R
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@@ -44,7 +44,7 @@ Terms <- read.delim(file = sgd_terms_tfile,
col.names = c("GO_ID", "GO_Term", "GO_Aspect", "GO_Term_Definition")
)
XX3 <- read.csv(file = all_sgd_terms_csv, stringsAsFactors = FALSE, header = TRUE)
XX3[, 1] <- paste("GO:", formatC(XX3[, 1], width = 7, flag = "0"), sep = "")
XX3[, 1] <- paste0("GO:", formatC(XX3[, 1], width = 7, flag = "0"))
XX3[, 2] <- gsub(pattern = " ", replacement = "_", x = XX3[, 2])
XX3[, 2] <- gsub(pattern = "/", replacement = "_", x = XX3[, 2])
@@ -84,7 +84,7 @@ if (length(study_nums) > 0) {
X1$Rank_L <- rank(X1$Z_lm_L)
X1$Rank_K <- rank(X1$Z_lm_K)
X1 <- X1[order(X1$OrfRep, decreasing = FALSE), ]
colnames(X1) <- paste(colnames(X1), "_X1", sep = "")
colnames(X1) <- paste0(colnames(X1), "_X1")
}
if (length(study_nums) > 1) {
@@ -111,7 +111,7 @@ if (length(study_nums) > 1) {
X2$Rank_K <- rank(X2$Z_lm_K)
X2 <- X2[order(X2$OrfRep, decreasing = FALSE), ]
colnames(X2) <- paste(colnames(X2), "_X2", sep = "")
colnames(X2) <- paste0(colnames(X2), "_X2")
X <- cbind(X1, X2)
}
@@ -138,7 +138,7 @@ if (length(study_nums) > 2) {
X3$Rank_L <- rank(X3$Z_lm_L)
X3$Rank_K <- rank(X3$Z_lm_K)
X3 <- X3[order(X3$OrfRep, decreasing = FALSE), ]
colnames(X3) <- paste(colnames(X3), "_X3", sep = "")
colnames(X3) <- paste0(colnames(X3), "_X3")
X <- cbind(X, X3)
}
@@ -165,7 +165,7 @@ if (length(study_nums) > 3) {
X4$Rank_L <- rank(X4$Z_lm_L)
X4$Rank_K <- rank(X4$Z_lm_K)
X4 <- X4[order(X4$OrfRep, decreasing = FALSE), ]
colnames(X4) <- paste(colnames(X4), "_X4", sep = "")
colnames(X4) <- paste0(colnames(X4), "_X4")
X <- cbind(X, X4)
}
@@ -192,7 +192,7 @@ if (length(study_nums) > 4) {
X5$Rank_L <- rank(X5$Z_lm_L)
X5$Rank_K <- rank(X5$Z_lm_K)
X5 <- X5[order(X5$OrfRep, decreasing = FALSE), ]
colnames(X5) <- paste(colnames(X5), "_X5", sep = "")
colnames(X5) <- paste0(colnames(X5), "_X5")
X <- cbind(X, X5)
}
@@ -441,7 +441,7 @@ for (s in 1:dim(XX3)[1]) {
if (Parent_Size > 2000) {
pdf(
file = file.path(output_dir, paste(XX3[s, 2], ".pdf", sep = "")),
file = file.path(output_dir, paste0(XX3[s, 2], ".pdf")),
width = 12,
height = 45,
onefile = TRUE
@@ -477,7 +477,7 @@ for (s in 1:dim(XX3)[1]) {
if (Parent_Size >= 1000 && Parent_Size <= 2000) {
pdf(
file = file.path(output_dir, paste(XX3[s, 2], ".pdf", sep = "")),
file = file.path(output_dir, paste0(XX3[s, 2], ".pdf")),
width = 12,
height = 35,
onefile = TRUE
@@ -513,7 +513,7 @@ for (s in 1:dim(XX3)[1]) {
if (Parent_Size >= 500 && Parent_Size <= 1000) {
pdf(
file = file.path(output_dir, paste(XX3[s, 2], ".pdf", sep = "")),
file = file.path(output_dir, paste0(XX3[s, 2], ".pdf")),
width = 12,
height = 30,
onefile = TRUE
@@ -549,7 +549,7 @@ for (s in 1:dim(XX3)[1]) {
if (Parent_Size >= 200 && Parent_Size <= 500) {
pdf(
file = file.path(output_dir, paste(XX3[s, 2], ".pdf", sep = "")),
file = file.path(output_dir, paste0(XX3[s, 2], ".pdf")),
width = 12,
height = 25,
onefile = TRUE
@@ -585,7 +585,7 @@ for (s in 1:dim(XX3)[1]) {
if (Parent_Size >= 100 && Parent_Size <= 200) {
pdf(
file = file.path(output_dir, paste(XX3[s, 2], ".pdf", sep = "")),
file = file.path(output_dir, paste0(XX3[s, 2], ".pdf")),
width = 12,
height = 20,
onefile = TRUE
@@ -621,7 +621,7 @@ for (s in 1:dim(XX3)[1]) {
if (Parent_Size >= 60 && Parent_Size <= 100) {
pdf(
file = file.path(output_dir, paste(XX3[s, 2], ".pdf", sep = "")),
file = file.path(output_dir, paste0(XX3[s, 2], ".pdf")),
width = 12,
height = 15,
onefile = TRUE
@@ -657,7 +657,7 @@ for (s in 1:dim(XX3)[1]) {
if (Parent_Size >= 30 && Parent_Size <= 60) {
pdf(
file = file.path(output_dir, paste(XX3[s, 2], ".pdf", sep = "")),
file = file.path(output_dir, paste0(XX3[s, 2], ".pdf")),
width = 12,
height = 10,
onefile = TRUE
@@ -709,7 +709,7 @@ for (s in 1:dim(XX3)[1]) {
if (Parent_Size >= 3 && Parent_Size <= 30) {
pdf(
file = file.path(output_dir, paste(XX3[s, 2], ".pdf", sep = "")),
file = file.path(output_dir, paste0(XX3[s, 2], ".pdf")),
width = 12,
height = 7,
onefile = TRUE
@@ -760,7 +760,7 @@ for (s in 1:dim(XX3)[1]) {
if (Parent_Size == 2) {
pdf(
file = file.path(output_dir, paste(XX3[s, 2], ".pdf", sep = "")),
file = file.path(output_dir, paste0(XX3[s, 2], ".pdf")),
width = 12,
height = 7,
onefile = TRUE