R/mutations.R
In seanchen607/deplink: Compares the genetic/epigenetic features between cancer cell lines with different dependencies of a gene set (signature)
Defines functions
mutations
Documented in
mutations
##' 'mutations' compares the genetic mutations between cancer cell lines with highest and lowest dependencies of a gene set (signature).
##'
##'
##' @title mutations
##' @param signature.name Names of a signature (format: character)
##' @param signature Gene names of a signature (format: vector)
##' @param cutoff.freq Cutoff for frequency of cancer cell lines for each cancer type, default 10
##' @param cutoff.percentile Cutoff for percentile of cancer cell lines with highest/lowest dependency, default 0.2
##' @param cutoff.pvalue Cutoff for p-value of the T-test results, default 0.05
##' @param cutoff.diff Cutoff for difference of the T-test results, default 0.1
##' @return plot
##' @importFrom stats complete.cases
##' @importFrom wesanderson wes_palette
##' @importFrom cowplot plot_grid
##' @importFrom purrr map
##' @importFrom ggrepel geom_label_repel
##' @import data.table ggpubr ggplot2
##' @export
##' @author Xiao Chen
##' @references 1. X Chen, J McGuire, F Zhu, X Xu, Y Li, D Karagiannis, R Dalla-Favera, A Ciccia, J Amengual, C Lu (2020).
##' Harnessing genetic dependency correlation network to reveal chromatin vulnerability in cancer.
##' In preparation.
##' @examples
##' source(system.file("script", "load_libs.R", package = "deplink"))
##' signature.name = "9-1-1"
##' signature = c("RAD9A", "RAD1", "HUS1", "RAD17")
##' mutations(signature.name, signature)
## Main
mutations <- function(signature.name,
signature,
cutoff.freq = 10,
cutoff.percentile = 0.2,
cutoff.pvalue = 0.05,
cutoff.diff = 0.1
) {
# Primary.Disease.freq = table(dep.t.signature.meta.order$disease)
Primary.Disease.freq = table(dep.t.meta$tcga_code)
Primary.Disease.freq.cutoff = Primary.Disease.freq[Primary.Disease.freq >= cutoff.freq]
TCGA.tumor.target = TCGA.tumor[TCGA.tumor$tcga_code %in% names(Primary.Disease.freq.cutoff),,drop=FALSE]
head(TCGA.tumor.target)
dim(TCGA.tumor.target)
# 1047 1
dep.t = dep.t[rownames(dep.t) %in% rownames(TCGA.tumor.target),,drop=FALSE]
head(dep.t)
dim(dep.t)
# 458 18333
dep.t.signature = dep.t[,colnames(dep.t) %in% signature, drop=FALSE]
dep.t.signature$signature.score = rowMeans(dep.t.signature)*(-1)
dep.t.signature = dep.t.signature[order(dep.t.signature$signature.score, decreasing=TRUE),]
head(dep.t.signature)
dim(dep.t.signature)
# 558 5
dep.t.signature.high = dep.t.signature[1:ceiling(nrow(dep.t.signature)*cutoff.percentile),,drop=FALSE]
head(dep.t.signature.high)
dim(dep.t.signature.high)
# 56 12
dep.t.signature.low = dep.t.signature[(nrow(dep.t.signature)-ceiling(nrow(dep.t.signature)*cutoff.percentile) + 1):nrow(dep.t.signature),,drop=FALSE]
head(dep.t.signature.low)
dim(dep.t.signature.low)
# 56 12
# write.csv(dep.t.signature, paste0("dep_", signature.name, "_score.csv"))
# write.csv(dep.t.signature.high, paste0("dep_", signature.name, "_score.high", cutoff.percentile, ".csv"))
# write.csv(dep.t.signature.low, paste0("dep_", signature.name, "_score.low", cutoff.percentile, ".csv"))
#############################################
# Mutation
mutation.signature.high = mutation[rownames(mutation) %in% rownames(dep.t.signature.high),,drop=FALSE]
mutation.signature.high.gene = mutation.signature.high[,colSums(mutation.signature.high)>1]
mutation.signature.high$signature = paste0(signature.name, ".dep.high")
head(mutation.signature.high)
dim(mutation.signature.high)
# 40 44
mutation.signature.low = mutation[rownames(mutation) %in% rownames(dep.t.signature.low),,drop=FALSE]
mutation.signature.low.gene = mutation.signature.low[,colSums(mutation.signature.low)>1]
mutation.signature.low$signature = paste0(signature.name, ".dep.low")
head(mutation.signature.low)
dim(mutation.signature.low)
# 46 44
mutation.signature.mid = mutation[!rownames(mutation) %in% c(rownames(dep.t.signature.high), rownames(dep.t.signature.low)),,drop=FALSE]
mutation.signature.mid.gene = mutation.signature.mid[,colSums(mutation.signature.mid)>1]
mutation.signature.mid$signature = paste0(signature.name, ".dep.mid")
head(mutation.signature.mid)
dim(mutation.signature.mid)
# 360 44
gene.union = Reduce(union, list(colnames(mutation.signature.high.gene), colnames(mutation.signature.low.gene), colnames(mutation.signature.mid.gene)))
length(gene.union)
# 9422
mutation.signature = rbind(mutation.signature.high, mutation.signature.mid, mutation.signature.low)
mutation.signature = mutation.signature[,colnames(mutation.signature) %in% c(gene.union, "signature"),drop=FALSE]
head(mutation.signature)
dim(mutation.signature)
# 554 9423
# write.csv(mutation.signature, paste0("mutation/dep_", signature.name, "_hml", cutoff.percentile, "_mutation.csv"), quote=FALSE)
mutation.high = mutation.signature[mutation.signature$signature %like% "high",,drop=FALSE]
head(mutation.high)
dim(mutation.high)
# 40 44
mutation.mid = mutation.signature[mutation.signature$signature %like% "mid",,drop=FALSE]
mutation.low = mutation.signature[mutation.signature$signature %like% "low",,drop=FALSE]
# signature.high
mutation.high.p = apply(mutation.signature[1:(ncol(mutation.signature)-1)], 2, function(x) signif(t.test(na.omit(x[1:nrow(mutation.high)]), na.omit(x[(nrow(mutation.high)+1):nrow(mutation.signature)]))$p.value,5))
head(mutation.high.p)
length(mutation.high.p)
# 42
mutation.high.q = signif(p.adjust(mutation.high.p, "BH"),5)
head(mutation.high.q)
length(mutation.high.q)
# 42
mutation.high.mean1 = apply(mutation.signature[1:(ncol(mutation.signature)-1)], 2, function(x) signif(mean(na.omit(x[1:nrow(mutation.high)])), 5))
mutation.high.mean2 = apply(mutation.signature[1:(ncol(mutation.signature)-1)], 2, function(x) signif(mean(na.omit(x[(nrow(mutation.high)+1):nrow(mutation.signature)])), 5))
mutation.high.diff = apply(mutation.signature[1:(ncol(mutation.signature)-1)], 2, function(x) signif(mean(na.omit(x[1:nrow(mutation.high)])) - mean(na.omit(x[(nrow(mutation.high)+1):nrow(mutation.signature)])), 5))
head(mutation.high.diff)
length(mutation.high.diff)
# 42
mutation.high.deg = data.frame(mutation.high.mean1, mutation.high.mean2, mutation.high.diff, mutation.high.p, mutation.high.q, row.names=names(mutation.high.diff))
colnames(mutation.high.deg) = c("mutation.high", "mutation.other", "diff.high2other", "pvalue", "qvalue")
head(mutation.high.deg)
dim(mutation.high.deg)
# 42 5
# write.csv(mutation.high.deg, paste0("mutation/dep_", signature.name, "_hml", cutoff.percentile, "_mutation.high.deg.csv"), quote=FALSE)
# signature.low
mutation.low.p = apply(mutation.signature[1:(ncol(mutation.signature)-1)], 2, function(x) signif(t.test(x[1:(nrow(mutation.signature)-nrow(mutation.low))], x[(nrow(mutation.signature)-nrow(mutation.low)+1):nrow(mutation.signature)])$p.value,5))
head(mutation.low.p)
length(mutation.low.p)
# 42
mutation.low.q = signif(p.adjust(mutation.low.p, "BH"),5)
head(mutation.low.q)
length(mutation.low.q)
# 42
mutation.low.mean1 = apply(mutation.signature[1:(ncol(mutation.signature)-1)], 2, function(x) signif(mean(na.omit(x[(nrow(mutation.signature)-nrow(mutation.low)+1):nrow(mutation.signature)])), 5))
mutation.low.mean2 = apply(mutation.signature[1:(ncol(mutation.signature)-1)], 2, function(x) signif(mean(na.omit(x[1:(nrow(mutation.signature)-nrow(mutation.low))])), 5))
mutation.low.diff = apply(mutation.signature[1:(ncol(mutation.signature)-1)], 2, function(x) signif(mean(na.omit(x[(nrow(mutation.signature)-nrow(mutation.low)+1):nrow(mutation.signature)])) - mean(na.omit(x[1:(nrow(mutation.signature)-nrow(mutation.low))])), 5))
head(mutation.low.diff)
length(mutation.low.diff)
# 42
mutation.low.deg = data.frame(mutation.low.mean1, mutation.low.mean2, mutation.low.diff, mutation.low.p, mutation.low.q, row.names=names(mutation.low.diff))
colnames(mutation.low.deg) = c("mutation.low", "mutation.other", "diff.low2other", "pvalue", "qvalue")
head(mutation.low.deg)
dim(mutation.low.deg)
# 42 5
# write.csv(mutation.low.deg, paste0("mutation/dep_", signature.name, "_hml", cutoff.percentile, "_mutation.low.deg.csv"), quote=FALSE)
# signature.high2low
mutation.high2low.p = apply(mutation.signature[1:(ncol(mutation.signature)-1)], 2, function(x) signif(t.test(na.omit(x[1:nrow(mutation.high)]), na.omit(x[(nrow(mutation.signature)-nrow(mutation.low)+1):nrow(mutation.signature)]))$p.value,5))
head(mutation.high2low.p)
length(mutation.high2low.p)
# 42
mutation.high2low.q = signif(p.adjust(mutation.high2low.p, "BH"),5)
head(mutation.high2low.q)
length(mutation.high2low.q)
# 42
mutation.high2low.mean1 = apply(mutation.signature[1:(ncol(mutation.signature)-1)], 2, function(x) signif(mean(na.omit(x[1:nrow(mutation.high)])), 5))
mutation.high2low.mean2 = apply(mutation.signature[1:(ncol(mutation.signature)-1)], 2, function(x) signif(mean(na.omit(x[(nrow(mutation.signature)-nrow(mutation.low)+1):nrow(mutation.signature)])), 5))
mutation.high2low.diff = mutation.high2low.mean1 - mutation.high2low.mean2
head(mutation.high2low.diff)
length(mutation.high2low.diff)
# 42
mutation.high2low.deg = data.frame(mutation.high2low.mean1, mutation.high2low.mean2, mutation.high2low.diff, mutation.high2low.p, mutation.high2low.q, row.names=names(mutation.high2low.diff))
colnames(mutation.high2low.deg) = c("mutation.high", "mutation.low", "diff.high2low", "pvalue", "qvalue")
head(mutation.high2low.deg)
dim(mutation.high2low.deg)
# 42 5
# write.csv(mutation.high2low.deg, paste0("mutation/dep_", signature.name, "_hml", cutoff.percentile, "_mutation.high2low.deg.csv"), quote=FALSE)
# mutation.high.deg = mutation.high.deg[mutation.high.deg$mutation.high > 0 & mutation.high.deg$mutation.other > 0,,drop=FALSE]
# mutation.low.deg = mutation.low.deg[mutation.low.deg$mutation.low > 0 & mutation.low.deg$mutation.other > 0,,drop=FALSE]
# cutoff.pvalue = 0.05
# cutoff.diff = 0.1
set.seed(42)
p1 <- ggplot(data = mutation.high.deg, mapping = aes(x = diff.high2other, y = (-1)*log(pvalue, 10))) +
geom_point(size=1, color= ifelse(mutation.high.deg$pvalue < cutoff.pvalue & mutation.high.deg$diff.high2other > cutoff.diff, "red", ifelse(mutation.high.deg$pvalue < cutoff.pvalue & mutation.high.deg$diff.high2other < cutoff.diff*(-1), "blue", "grey60")))+
# xlim(-0.2,0.2) +
# ylim(0,4) +
geom_hline(yintercept = (-1)*log(cutoff.pvalue, 10), linetype="dashed", colour="grey30", size=0.2) +
geom_vline(xintercept = cutoff.diff, linetype="dashed", colour="grey30", size=0.2) +
geom_vline(xintercept = (-1)*cutoff.diff, linetype="dashed", colour="grey30", size=0.2) +
annotate("text", x=-0.2, y=max((-1)*log(mutation.high.deg$pvalue, 10))*1.1, parse=FALSE, label = paste0("Signature.high cell lines: ", nrow(mutation.signature.high)), color = "red", hjust = 0) +
geom_label_repel(aes(label=ifelse(mutation.high.deg$pvalue < cutoff.pvalue & abs(mutation.high.deg$diff.high2other) > cutoff.diff, as.character(rownames(mutation.high.deg)), "")), size = 2, color = ifelse(mutation.high.deg$diff.high2other > 0, "red", "blue"), segment.size=0.2) +
labs(x="Mutation difference", y="-log10(p value)", title=paste0("Signature [", signature.name, "] High vs. others"))
p1 <- p1 + theme_classic() + rremove("legend")
# p1
p2 <- ggplot(data = mutation.low.deg, mapping = aes(x = diff.low2other, y = (-1)*log(pvalue, 10))) +
geom_point(size=1, color= ifelse(mutation.low.deg$pvalue < cutoff.pvalue & mutation.low.deg$diff.low2other > cutoff.diff, "red", ifelse(mutation.low.deg$pvalue < cutoff.pvalue & mutation.low.deg$diff.low2other < cutoff.diff*(-1), "blue", "grey60")))+
# xlim(-0.2,0.2) +
# ylim(0,4) +
geom_hline(yintercept = (-1)*log(cutoff.pvalue, 10), linetype="dashed", colour="grey30", size=0.2) +
geom_vline(xintercept = cutoff.diff, linetype="dashed", colour="grey30", size=0.2) +
geom_vline(xintercept = (-1)*cutoff.diff, linetype="dashed", colour="grey30", size=0.2) +
annotate("text", x=-0.2, y=max((-1)*log(mutation.low.deg$pvalue, 10))*1.1, parse=FALSE, label = paste0("Signature.low cell lines: ", nrow(mutation.signature.low)), color = "red", hjust = 0) +
geom_label_repel(aes(label=ifelse(mutation.low.deg$pvalue < cutoff.pvalue & abs(mutation.low.deg$diff.low2other) > cutoff.diff, as.character(rownames(mutation.low.deg)), "")), size = 2, color = ifelse(mutation.low.deg$diff.low2other > 0, "red", "blue"), segment.size=0.2) +
labs(x="Mutation difference", y="-log10(p value)", title=paste0("Signature [", signature.name, "] Low vs. others"))
p2 <- p2 + theme_classic() + rremove("legend")
# p2
p3 <- ggplot(data = mutation.high2low.deg, mapping = aes(x = diff.high2low, y = (-1)*log(pvalue, 10))) +
geom_point(size=1, color= ifelse(mutation.high2low.deg$pvalue < cutoff.pvalue & mutation.high2low.deg$diff.high2low > cutoff.diff, "red", ifelse(mutation.high2low.deg$pvalue < cutoff.pvalue & mutation.high2low.deg$diff.high2low < cutoff.diff*(-1), "blue", "grey60")))+
# xlim(-0.2,0.2) +
# ylim(0,4) +
geom_hline(yintercept = (-1)*log(cutoff.pvalue, 10), linetype="dashed", colour="grey30", size=0.2) +
geom_vline(xintercept = cutoff.diff, linetype="dashed", colour="grey30", size=0.2) +
geom_vline(xintercept = (-1)*cutoff.diff, linetype="dashed", colour="grey30", size=0.2) +
annotate("text", x=-0.2, y=max((-1)*log(mutation.high2low.deg$pvalue, 10))*1.1, parse=FALSE, label = paste0("Signature.high/low cell lines: ", nrow(mutation.signature.high), "/", nrow(mutation.signature.low)), color = "red", hjust = 0) +
geom_label_repel(aes(label=ifelse(mutation.high2low.deg$pvalue < cutoff.pvalue & abs(mutation.high2low.deg$diff.high2low) > cutoff.diff, as.character(rownames(mutation.high2low.deg)), "")), size = 2, color = ifelse(mutation.high2low.deg$diff.high2low > 0, "red", "blue"), segment.size=0.2) +
labs(x="Mutation difference", y="-log10(p value)", title=paste0("Signature [", signature.name, "] High vs. Low"))
p3 <- p3 + theme_classic() + rremove("legend")
# p3
# Arranging the plot using cowplot
p = suppressWarnings(plot_grid(p1, p2, p3, ncol = 3, align = "hv", rel_widths = c(1,1), rel_heights = c(1,1)))
# p <- ggplotGrob(p)
return(p)
}
seanchen607/deplink documentation built on Nov. 18, 2020, 11:15 a.m.
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Defines functions mutations
Documented in mutations
##' 'mutations' compares the genetic mutations between cancer cell lines with highest and lowest dependencies of a gene set (signature).
##'
##'
##' @title mutations
##' @param signature.name Names of a signature (format: character)
##' @param signature Gene names of a signature (format: vector)
##' @param cutoff.freq Cutoff for frequency of cancer cell lines for each cancer type, default 10
##' @param cutoff.percentile Cutoff for percentile of cancer cell lines with highest/lowest dependency, default 0.2
##' @param cutoff.pvalue Cutoff for p-value of the T-test results, default 0.05
##' @param cutoff.diff Cutoff for difference of the T-test results, default 0.1
##' @return plot
##' @importFrom stats complete.cases
##' @importFrom wesanderson wes_palette
##' @importFrom cowplot plot_grid
##' @importFrom purrr map
##' @importFrom ggrepel geom_label_repel
##' @import data.table ggpubr ggplot2
##' @export
##' @author Xiao Chen
##' @references 1. X Chen, J McGuire, F Zhu, X Xu, Y Li, D Karagiannis, R Dalla-Favera, A Ciccia, J Amengual, C Lu (2020).
##' Harnessing genetic dependency correlation network to reveal chromatin vulnerability in cancer.
##' In preparation.
##' @examples
##' source(system.file("script", "load_libs.R", package = "deplink"))
##' signature.name = "9-1-1"
##' signature = c("RAD9A", "RAD1", "HUS1", "RAD17")
##' mutations(signature.name, signature)
## Main
mutations <- function(signature.name,
signature,
cutoff.freq = 10,
cutoff.percentile = 0.2,
cutoff.pvalue = 0.05,
cutoff.diff = 0.1
) {
# Primary.Disease.freq = table(dep.t.signature.meta.order$disease)
Primary.Disease.freq = table(dep.t.meta$tcga_code)
Primary.Disease.freq.cutoff = Primary.Disease.freq[Primary.Disease.freq >= cutoff.freq]
TCGA.tumor.target = TCGA.tumor[TCGA.tumor$tcga_code %in% names(Primary.Disease.freq.cutoff),,drop=FALSE]
head(TCGA.tumor.target)
dim(TCGA.tumor.target)
# 1047 1
dep.t = dep.t[rownames(dep.t) %in% rownames(TCGA.tumor.target),,drop=FALSE]
head(dep.t)
dim(dep.t)
# 458 18333
dep.t.signature = dep.t[,colnames(dep.t) %in% signature, drop=FALSE]
dep.t.signature$signature.score = rowMeans(dep.t.signature)*(-1)
dep.t.signature = dep.t.signature[order(dep.t.signature$signature.score, decreasing=TRUE),]
head(dep.t.signature)
dim(dep.t.signature)
# 558 5
dep.t.signature.high = dep.t.signature[1:ceiling(nrow(dep.t.signature)*cutoff.percentile),,drop=FALSE]
head(dep.t.signature.high)
dim(dep.t.signature.high)
# 56 12
dep.t.signature.low = dep.t.signature[(nrow(dep.t.signature)-ceiling(nrow(dep.t.signature)*cutoff.percentile) + 1):nrow(dep.t.signature),,drop=FALSE]
head(dep.t.signature.low)
dim(dep.t.signature.low)
# 56 12
# write.csv(dep.t.signature, paste0("dep_", signature.name, "_score.csv"))
# write.csv(dep.t.signature.high, paste0("dep_", signature.name, "_score.high", cutoff.percentile, ".csv"))
# write.csv(dep.t.signature.low, paste0("dep_", signature.name, "_score.low", cutoff.percentile, ".csv"))
#############################################
# Mutation
mutation.signature.high = mutation[rownames(mutation) %in% rownames(dep.t.signature.high),,drop=FALSE]
mutation.signature.high.gene = mutation.signature.high[,colSums(mutation.signature.high)>1]
mutation.signature.high$signature = paste0(signature.name, ".dep.high")
head(mutation.signature.high)
dim(mutation.signature.high)
# 40 44
mutation.signature.low = mutation[rownames(mutation) %in% rownames(dep.t.signature.low),,drop=FALSE]
mutation.signature.low.gene = mutation.signature.low[,colSums(mutation.signature.low)>1]
mutation.signature.low$signature = paste0(signature.name, ".dep.low")
head(mutation.signature.low)
dim(mutation.signature.low)
# 46 44
mutation.signature.mid = mutation[!rownames(mutation) %in% c(rownames(dep.t.signature.high), rownames(dep.t.signature.low)),,drop=FALSE]
mutation.signature.mid.gene = mutation.signature.mid[,colSums(mutation.signature.mid)>1]
mutation.signature.mid$signature = paste0(signature.name, ".dep.mid")
head(mutation.signature.mid)
dim(mutation.signature.mid)
# 360 44
gene.union = Reduce(union, list(colnames(mutation.signature.high.gene), colnames(mutation.signature.low.gene), colnames(mutation.signature.mid.gene)))
length(gene.union)
# 9422
mutation.signature = rbind(mutation.signature.high, mutation.signature.mid, mutation.signature.low)
mutation.signature = mutation.signature[,colnames(mutation.signature) %in% c(gene.union, "signature"),drop=FALSE]
head(mutation.signature)
dim(mutation.signature)
# 554 9423
# write.csv(mutation.signature, paste0("mutation/dep_", signature.name, "_hml", cutoff.percentile, "_mutation.csv"), quote=FALSE)
mutation.high = mutation.signature[mutation.signature$signature %like% "high",,drop=FALSE]
head(mutation.high)
dim(mutation.high)
# 40 44
mutation.mid = mutation.signature[mutation.signature$signature %like% "mid",,drop=FALSE]
mutation.low = mutation.signature[mutation.signature$signature %like% "low",,drop=FALSE]
# signature.high
mutation.high.p = apply(mutation.signature[1:(ncol(mutation.signature)-1)], 2, function(x) signif(t.test(na.omit(x[1:nrow(mutation.high)]), na.omit(x[(nrow(mutation.high)+1):nrow(mutation.signature)]))$p.value,5))
head(mutation.high.p)
length(mutation.high.p)
# 42
mutation.high.q = signif(p.adjust(mutation.high.p, "BH"),5)
head(mutation.high.q)
length(mutation.high.q)
# 42
mutation.high.mean1 = apply(mutation.signature[1:(ncol(mutation.signature)-1)], 2, function(x) signif(mean(na.omit(x[1:nrow(mutation.high)])), 5))
mutation.high.mean2 = apply(mutation.signature[1:(ncol(mutation.signature)-1)], 2, function(x) signif(mean(na.omit(x[(nrow(mutation.high)+1):nrow(mutation.signature)])), 5))
mutation.high.diff = apply(mutation.signature[1:(ncol(mutation.signature)-1)], 2, function(x) signif(mean(na.omit(x[1:nrow(mutation.high)])) - mean(na.omit(x[(nrow(mutation.high)+1):nrow(mutation.signature)])), 5))
head(mutation.high.diff)
length(mutation.high.diff)
# 42
mutation.high.deg = data.frame(mutation.high.mean1, mutation.high.mean2, mutation.high.diff, mutation.high.p, mutation.high.q, row.names=names(mutation.high.diff))
colnames(mutation.high.deg) = c("mutation.high", "mutation.other", "diff.high2other", "pvalue", "qvalue")
head(mutation.high.deg)
dim(mutation.high.deg)
# 42 5
# write.csv(mutation.high.deg, paste0("mutation/dep_", signature.name, "_hml", cutoff.percentile, "_mutation.high.deg.csv"), quote=FALSE)
# signature.low
mutation.low.p = apply(mutation.signature[1:(ncol(mutation.signature)-1)], 2, function(x) signif(t.test(x[1:(nrow(mutation.signature)-nrow(mutation.low))], x[(nrow(mutation.signature)-nrow(mutation.low)+1):nrow(mutation.signature)])$p.value,5))
head(mutation.low.p)
length(mutation.low.p)
# 42
mutation.low.q = signif(p.adjust(mutation.low.p, "BH"),5)
head(mutation.low.q)
length(mutation.low.q)
# 42
mutation.low.mean1 = apply(mutation.signature[1:(ncol(mutation.signature)-1)], 2, function(x) signif(mean(na.omit(x[(nrow(mutation.signature)-nrow(mutation.low)+1):nrow(mutation.signature)])), 5))
mutation.low.mean2 = apply(mutation.signature[1:(ncol(mutation.signature)-1)], 2, function(x) signif(mean(na.omit(x[1:(nrow(mutation.signature)-nrow(mutation.low))])), 5))
mutation.low.diff = apply(mutation.signature[1:(ncol(mutation.signature)-1)], 2, function(x) signif(mean(na.omit(x[(nrow(mutation.signature)-nrow(mutation.low)+1):nrow(mutation.signature)])) - mean(na.omit(x[1:(nrow(mutation.signature)-nrow(mutation.low))])), 5))
head(mutation.low.diff)
length(mutation.low.diff)
# 42
mutation.low.deg = data.frame(mutation.low.mean1, mutation.low.mean2, mutation.low.diff, mutation.low.p, mutation.low.q, row.names=names(mutation.low.diff))
colnames(mutation.low.deg) = c("mutation.low", "mutation.other", "diff.low2other", "pvalue", "qvalue")
head(mutation.low.deg)
dim(mutation.low.deg)
# 42 5
# write.csv(mutation.low.deg, paste0("mutation/dep_", signature.name, "_hml", cutoff.percentile, "_mutation.low.deg.csv"), quote=FALSE)
# signature.high2low
mutation.high2low.p = apply(mutation.signature[1:(ncol(mutation.signature)-1)], 2, function(x) signif(t.test(na.omit(x[1:nrow(mutation.high)]), na.omit(x[(nrow(mutation.signature)-nrow(mutation.low)+1):nrow(mutation.signature)]))$p.value,5))
head(mutation.high2low.p)
length(mutation.high2low.p)
# 42
mutation.high2low.q = signif(p.adjust(mutation.high2low.p, "BH"),5)
head(mutation.high2low.q)
length(mutation.high2low.q)
# 42
mutation.high2low.mean1 = apply(mutation.signature[1:(ncol(mutation.signature)-1)], 2, function(x) signif(mean(na.omit(x[1:nrow(mutation.high)])), 5))
mutation.high2low.mean2 = apply(mutation.signature[1:(ncol(mutation.signature)-1)], 2, function(x) signif(mean(na.omit(x[(nrow(mutation.signature)-nrow(mutation.low)+1):nrow(mutation.signature)])), 5))
mutation.high2low.diff = mutation.high2low.mean1 - mutation.high2low.mean2
head(mutation.high2low.diff)
length(mutation.high2low.diff)
# 42
mutation.high2low.deg = data.frame(mutation.high2low.mean1, mutation.high2low.mean2, mutation.high2low.diff, mutation.high2low.p, mutation.high2low.q, row.names=names(mutation.high2low.diff))
colnames(mutation.high2low.deg) = c("mutation.high", "mutation.low", "diff.high2low", "pvalue", "qvalue")
head(mutation.high2low.deg)
dim(mutation.high2low.deg)
# 42 5
# write.csv(mutation.high2low.deg, paste0("mutation/dep_", signature.name, "_hml", cutoff.percentile, "_mutation.high2low.deg.csv"), quote=FALSE)
# mutation.high.deg = mutation.high.deg[mutation.high.deg$mutation.high > 0 & mutation.high.deg$mutation.other > 0,,drop=FALSE]
# mutation.low.deg = mutation.low.deg[mutation.low.deg$mutation.low > 0 & mutation.low.deg$mutation.other > 0,,drop=FALSE]
# cutoff.pvalue = 0.05
# cutoff.diff = 0.1
set.seed(42)
p1 <- ggplot(data = mutation.high.deg, mapping = aes(x = diff.high2other, y = (-1)*log(pvalue, 10))) +
geom_point(size=1, color= ifelse(mutation.high.deg$pvalue < cutoff.pvalue & mutation.high.deg$diff.high2other > cutoff.diff, "red", ifelse(mutation.high.deg$pvalue < cutoff.pvalue & mutation.high.deg$diff.high2other < cutoff.diff*(-1), "blue", "grey60")))+
# xlim(-0.2,0.2) +
# ylim(0,4) +
geom_hline(yintercept = (-1)*log(cutoff.pvalue, 10), linetype="dashed", colour="grey30", size=0.2) +
geom_vline(xintercept = cutoff.diff, linetype="dashed", colour="grey30", size=0.2) +
geom_vline(xintercept = (-1)*cutoff.diff, linetype="dashed", colour="grey30", size=0.2) +
annotate("text", x=-0.2, y=max((-1)*log(mutation.high.deg$pvalue, 10))*1.1, parse=FALSE, label = paste0("Signature.high cell lines: ", nrow(mutation.signature.high)), color = "red", hjust = 0) +
geom_label_repel(aes(label=ifelse(mutation.high.deg$pvalue < cutoff.pvalue & abs(mutation.high.deg$diff.high2other) > cutoff.diff, as.character(rownames(mutation.high.deg)), "")), size = 2, color = ifelse(mutation.high.deg$diff.high2other > 0, "red", "blue"), segment.size=0.2) +
labs(x="Mutation difference", y="-log10(p value)", title=paste0("Signature [", signature.name, "] High vs. others"))
p1 <- p1 + theme_classic() + rremove("legend")
# p1
p2 <- ggplot(data = mutation.low.deg, mapping = aes(x = diff.low2other, y = (-1)*log(pvalue, 10))) +
geom_point(size=1, color= ifelse(mutation.low.deg$pvalue < cutoff.pvalue & mutation.low.deg$diff.low2other > cutoff.diff, "red", ifelse(mutation.low.deg$pvalue < cutoff.pvalue & mutation.low.deg$diff.low2other < cutoff.diff*(-1), "blue", "grey60")))+
# xlim(-0.2,0.2) +
# ylim(0,4) +
geom_hline(yintercept = (-1)*log(cutoff.pvalue, 10), linetype="dashed", colour="grey30", size=0.2) +
geom_vline(xintercept = cutoff.diff, linetype="dashed", colour="grey30", size=0.2) +
geom_vline(xintercept = (-1)*cutoff.diff, linetype="dashed", colour="grey30", size=0.2) +
annotate("text", x=-0.2, y=max((-1)*log(mutation.low.deg$pvalue, 10))*1.1, parse=FALSE, label = paste0("Signature.low cell lines: ", nrow(mutation.signature.low)), color = "red", hjust = 0) +
geom_label_repel(aes(label=ifelse(mutation.low.deg$pvalue < cutoff.pvalue & abs(mutation.low.deg$diff.low2other) > cutoff.diff, as.character(rownames(mutation.low.deg)), "")), size = 2, color = ifelse(mutation.low.deg$diff.low2other > 0, "red", "blue"), segment.size=0.2) +
labs(x="Mutation difference", y="-log10(p value)", title=paste0("Signature [", signature.name, "] Low vs. others"))
p2 <- p2 + theme_classic() + rremove("legend")
# p2
p3 <- ggplot(data = mutation.high2low.deg, mapping = aes(x = diff.high2low, y = (-1)*log(pvalue, 10))) +
geom_point(size=1, color= ifelse(mutation.high2low.deg$pvalue < cutoff.pvalue & mutation.high2low.deg$diff.high2low > cutoff.diff, "red", ifelse(mutation.high2low.deg$pvalue < cutoff.pvalue & mutation.high2low.deg$diff.high2low < cutoff.diff*(-1), "blue", "grey60")))+
# xlim(-0.2,0.2) +
# ylim(0,4) +
geom_hline(yintercept = (-1)*log(cutoff.pvalue, 10), linetype="dashed", colour="grey30", size=0.2) +
geom_vline(xintercept = cutoff.diff, linetype="dashed", colour="grey30", size=0.2) +
geom_vline(xintercept = (-1)*cutoff.diff, linetype="dashed", colour="grey30", size=0.2) +
annotate("text", x=-0.2, y=max((-1)*log(mutation.high2low.deg$pvalue, 10))*1.1, parse=FALSE, label = paste0("Signature.high/low cell lines: ", nrow(mutation.signature.high), "/", nrow(mutation.signature.low)), color = "red", hjust = 0) +
geom_label_repel(aes(label=ifelse(mutation.high2low.deg$pvalue < cutoff.pvalue & abs(mutation.high2low.deg$diff.high2low) > cutoff.diff, as.character(rownames(mutation.high2low.deg)), "")), size = 2, color = ifelse(mutation.high2low.deg$diff.high2low > 0, "red", "blue"), segment.size=0.2) +
labs(x="Mutation difference", y="-log10(p value)", title=paste0("Signature [", signature.name, "] High vs. Low"))
p3 <- p3 + theme_classic() + rremove("legend")
# p3
# Arranging the plot using cowplot
p = suppressWarnings(plot_grid(p1, p2, p3, ncol = 3, align = "hv", rel_widths = c(1,1), rel_heights = c(1,1)))
# p <- ggplotGrob(p)
return(p)
}
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