R/expressions.R
In seanchen607/deplink: Compares the genetic/epigenetic features between cancer cell lines with different dependencies of a gene set (signature)
Defines functions
expressions
Documented in
expressions
##' 'expressions' compares the gene expression between cancer cell lines with highest and lowest dependencies of a gene set (signature).
##'
##'
##' @title expressions
##' @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.qvalue Cutoff for q-value of the T-test results, default 0.1
##' @param cutoff.fc Cutoff for fold changes of the T-test results, default 2
##' @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")
##' expressions(signature.name, signature)
## Main
expressions <- function(signature.name,
signature,
cutoff.freq = 10,
cutoff.percentile = 0.2,
cutoff.qvalue = 0.1,
cutoff.fc = 2
) {
# 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$signature.score, decreasing=TRUE),]
head(dep.t.signature)
dim(dep.t.signature)
# 558 5
dep.t.signature.high = dep.t.signature[1:ceiling(nrow(dep.t.signature)*cutoff.percentile),,drop=FALSE]
head(dep.t.signature.high)
dim(dep.t.signature.high)
# 56 12
dep.t.signature.low = dep.t.signature[(nrow(dep.t.signature)-ceiling(nrow(dep.t.signature)*cutoff.percentile) + 1):nrow(dep.t.signature),,drop=FALSE]
head(dep.t.signature.low)
dim(dep.t.signature.low)
# 56 12
# write.csv(dep.t.signature, paste0("dep_", signature.name, "_score.csv"))
# write.csv(dep.t.signature.high, paste0("dep_", signature.name, "_score.high", cutoff.percentile, ".csv"))
# write.csv(dep.t.signature.low, paste0("dep_", signature.name, "_score.low", cutoff.percentile, ".csv"))
#############################################
# Expression
expression.share = exp.TPM.t
head(expression.share)
dim(expression.share)
# 554 16950
expression.share.signature.high = expression.share[rownames(expression.share) %in% rownames(dep.t.signature.high),,drop=FALSE]
expression.share.signature.high$signature = paste0(signature.name, ".dep.high")
head(expression.share.signature.high)
dim(expression.share.signature.high)
# 27 267
expression.share.signature.low = expression.share[rownames(expression.share) %in% rownames(dep.t.signature.low),,drop=FALSE]
expression.share.signature.low$signature = paste0(signature.name, ".dep.low")
head(expression.share.signature.low)
dim(expression.share.signature.low)
# 33 267
expression.share.signature.mid = expression.share[!rownames(expression.share) %in% c(rownames(dep.t.signature.high), rownames(dep.t.signature.low)),,drop=FALSE]
expression.share.signature.mid$signature = paste0(signature.name, ".dep.mid")
head(expression.share.signature.mid)
dim(expression.share.signature.mid)
# 267 267
expression.share.signature = rbind(expression.share.signature.high, expression.share.signature.mid, expression.share.signature.low)
head(expression.share.signature)
dim(expression.share.signature)
# 327 267
# write.csv(expression.share.signature, paste0("expression/dep_", signature.name, "_hml", cutoff.percentile, "_expression.csv"), quote=FALSE)
expression.high = expression.share.signature[expression.share.signature$signature %like% "high",,drop=FALSE]
head(expression.high)
dim(expression.high)
# 27 267
expression.mid = expression.share.signature[expression.share.signature$signature %like% "mid",,drop=FALSE]
expression.low = expression.share.signature[expression.share.signature$signature %like% "low",,drop=FALSE]
# signature.high
expression.high.p = apply(expression.share.signature[1:(ncol(expression.share.signature)-1)], 2, function(x) signif(t.test(x[1:nrow(expression.high)], x[(nrow(expression.high)+1):nrow(expression.share.signature)])$p.value,5))
head(expression.high.p)
length(expression.high.p)
# 266
expression.high.q = signif(p.adjust(expression.high.p, "BH"),5)
head(expression.high.q)
length(expression.high.q)
# 266
expression.high.mean1 = apply(expression.share.signature[1:(ncol(expression.share.signature)-1)], 2, function(x) signif(mean(na.omit(x[1:nrow(expression.high)])), 5))
expression.high.mean2 = apply(expression.share.signature[1:(ncol(expression.share.signature)-1)], 2, function(x) signif(mean(na.omit(x[(nrow(expression.high)+1):nrow(expression.share.signature)])), 5))
expression.high.fc = apply(expression.share.signature[1:(ncol(expression.share.signature)-1)], 2, function(x) signif(mean(na.omit(x[1:nrow(expression.high)])) / mean(na.omit(x[(nrow(expression.high)+1):nrow(expression.share.signature)])), 5))
head(expression.high.fc)
length(expression.high.fc)
# 266
expression.high.deg = data.frame(expression.high.mean1, expression.high.mean2, expression.high.fc, expression.high.p, expression.high.q, row.names=names(expression.high.fc))
colnames(expression.high.deg) = c("expression.high", "expression.other", "fc.high2other", "pvalue", "qvalue")
head(expression.high.deg)
dim(expression.high.deg)
# 4338 5
# write.csv(expression.high.deg, paste0("expression/dep_", signature.name, "_hml", cutoff.percentile, "_expression.high.deg.csv"), quote=TRUE)
# signature.low
expression.low.p = apply(expression.share.signature[1:(ncol(expression.share.signature)-1)], 2, function(x) signif(t.test(x[1:(nrow(expression.share.signature)-nrow(expression.low))], x[(nrow(expression.share.signature)-nrow(expression.low)+1):nrow(expression.share.signature)])$p.value,5))
head(expression.low.p)
length(expression.low.p)
# 266
expression.low.q = signif(p.adjust(expression.low.p, "BH"),5)
head(expression.low.q)
length(expression.low.q)
# 266
expression.low.mean1 = apply(expression.share.signature[1:(ncol(expression.share.signature)-1)], 2, function(x) signif(mean(na.omit(x[(nrow(expression.share.signature)-nrow(expression.low)+1):nrow(expression.share.signature)])), 5))
expression.low.mean2 = apply(expression.share.signature[1:(ncol(expression.share.signature)-1)], 2, function(x) signif(mean(na.omit(x[1:(nrow(expression.share.signature)-nrow(expression.low))])), 5))
expression.low.fc = apply(expression.share.signature[1:(ncol(expression.share.signature)-1)], 2, function(x) signif(mean(na.omit(x[(nrow(expression.share.signature)-nrow(expression.low)+1):nrow(expression.share.signature)])) / mean(na.omit(x[1:(nrow(expression.share.signature)-nrow(expression.low))])), 5))
head(expression.low.fc)
length(expression.low.fc)
# 266
expression.low.deg = data.frame(expression.low.mean1, expression.low.mean2, expression.low.fc, expression.low.p, expression.low.q, row.names=names(expression.low.fc))
colnames(expression.low.deg) = c("expression.low", "expression.other", "fc.low2other", "pvalue", "qvalue")
head(expression.low.deg)
dim(expression.low.deg)
# 4338 5
# write.csv(expression.low.deg, paste0("expression/dep_", signature.name, "_hml", cutoff.percentile, "_expression.low.deg.csv"), quote=TRUE)
# expression.high.deg = read.csv(paste0("expression/dep_", signature.name, "_hml", cutoff.percentile, "_expression.high.deg.csv"), header=TRUE, row.names=1)
# expression.low.deg = read.csv(paste0("expression/dep_", signature.name, "_hml", cutoff.percentile, "_expression.low.deg.csv"), header=TRUE, row.names=1)
# cutoff.qvalue = 0.1
# cutoff.fc = 2
set.seed(42)
p1 <- ggplot(data = expression.high.deg, mapping = aes(x = log(fc.high2other, 2), y = (-1)*log(qvalue, 10))) +
geom_point(size=0.5, color= ifelse(expression.high.deg$qvalue < cutoff.qvalue & expression.high.deg$fc.high2other > cutoff.fc, "red", ifelse(expression.high.deg$qvalue < cutoff.qvalue & expression.high.deg$fc.high2other < 1/cutoff.fc, "blue", "grey60")))+
# xlim(-1,1) +
# ylim(0,4) +
geom_hline(yintercept = (-1)*log(cutoff.qvalue, 10), linetype="dashed", colour="grey30", size=0.2) +
geom_vline(xintercept = log(cutoff.fc,2), linetype="dashed", colour="grey30", size=0.2) +
geom_vline(xintercept = (-1)*log(cutoff.fc,2), linetype="dashed", colour="grey30", size=0.2) +
annotate("text", x=min(log(expression.high.deg$fc.high2other[is.finite(expression.high.deg$fc.high2other) & expression.high.deg$fc.high2other > 0], 2))*0.9, y=max(na.omit((-1)*log(expression.low.deg$qvalue, 10)), na.omit((-1)*log(expression.high.deg$qvalue, 10)))*1.1, parse=FALSE, label = paste0("Signature.high cell lines: ", nrow(expression.share.signature.high)), color = "red", hjust = 0) +
# geom_label_repel(aes(label=ifelse(expression.high.deg$qvalue < (cutoff.qvalue) & abs(log(expression.high.deg$fc.high2other,2)) > log(cutoff.fc,2), as.character(rownames(expression.high.deg)), "")), size = 2, color = ifelse(expression.high.deg$fc.high2other < 0, "blue", "red"), segment.size=0.2) +
labs(x="Expression fold change (log2)", y="-log10(q value)", title=paste0("Signature [", signature.name, "] High vs. others"))
p1 <- p1 + rremove("legend") + theme_classic()
# p1
p2 <- ggplot(data = expression.low.deg, mapping = aes(x = log(fc.low2other, 2), y = (-1)*log(qvalue, 10))) +
geom_point(size=0.5, color= ifelse(expression.low.deg$qvalue < cutoff.qvalue & expression.low.deg$fc.low2other > cutoff.fc, "red", ifelse(expression.low.deg$qvalue < cutoff.qvalue & expression.low.deg$fc.low2other < 1/cutoff.fc, "blue", "grey60")))+
# xlim(-1,1) +
# ylim(0,4) +
geom_hline(yintercept = (-1)*log(cutoff.qvalue, 10), linetype="dashed", colour="grey30", size=0.2) +
geom_vline(xintercept = log(cutoff.fc,2), linetype="dashed", colour="grey30", size=0.2) +
geom_vline(xintercept = (-1)*log(cutoff.fc,2), linetype="dashed", colour="grey30", size=0.2) +
annotate("text", x=min(log(expression.low.deg$fc.low2other[is.finite(expression.low.deg$fc.low2other) & expression.low.deg$fc.low2other > 0], 2))*0.9, y=max(na.omit((-1)*log(expression.low.deg$qvalue, 10)), na.omit((-1)*log(expression.high.deg$qvalue, 10)))*1.1, parse=FALSE, label = paste0("Signature.low cell lines: ", nrow(expression.share.signature.low)), color = "red", hjust = 0) +
# geom_label_repel(aes(label=ifelse(expression.low.deg$qvalue < (cutoff.qvalue) & abs(log(expression.low.deg$fc.low2other,2)) > log(cutoff.fc,2), as.character(rownames(expression.low.deg)), "")), size = 2, color = ifelse(expression.low.deg$fc.low2other < 0, "blue", "red"), segment.size=0.2) +
labs(x="Expression fold change (log2)", y="-log10(q value)", title=paste0("Signature [", signature.name, "] Low vs. others"))
p2 <- p2 + rremove("legend") + theme_classic()
# p2
# Arranging the plot using cowplot
p = suppressWarnings(plot_grid(p1, p2, ncol = 2, 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 expressions
Documented in expressions
##' 'expressions' compares the gene expression between cancer cell lines with highest and lowest dependencies of a gene set (signature).
##'
##'
##' @title expressions
##' @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.qvalue Cutoff for q-value of the T-test results, default 0.1
##' @param cutoff.fc Cutoff for fold changes of the T-test results, default 2
##' @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")
##' expressions(signature.name, signature)
## Main
expressions <- function(signature.name,
signature,
cutoff.freq = 10,
cutoff.percentile = 0.2,
cutoff.qvalue = 0.1,
cutoff.fc = 2
) {
# 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"))
#############################################
# Expression
expression.share = exp.TPM.t
head(expression.share)
dim(expression.share)
# 554 16950
expression.share.signature.high = expression.share[rownames(expression.share) %in% rownames(dep.t.signature.high),,drop=FALSE]
expression.share.signature.high$signature = paste0(signature.name, ".dep.high")
head(expression.share.signature.high)
dim(expression.share.signature.high)
# 27 267
expression.share.signature.low = expression.share[rownames(expression.share) %in% rownames(dep.t.signature.low),,drop=FALSE]
expression.share.signature.low$signature = paste0(signature.name, ".dep.low")
head(expression.share.signature.low)
dim(expression.share.signature.low)
# 33 267
expression.share.signature.mid = expression.share[!rownames(expression.share) %in% c(rownames(dep.t.signature.high), rownames(dep.t.signature.low)),,drop=FALSE]
expression.share.signature.mid$signature = paste0(signature.name, ".dep.mid")
head(expression.share.signature.mid)
dim(expression.share.signature.mid)
# 267 267
expression.share.signature = rbind(expression.share.signature.high, expression.share.signature.mid, expression.share.signature.low)
head(expression.share.signature)
dim(expression.share.signature)
# 327 267
# write.csv(expression.share.signature, paste0("expression/dep_", signature.name, "_hml", cutoff.percentile, "_expression.csv"), quote=FALSE)
expression.high = expression.share.signature[expression.share.signature$signature %like% "high",,drop=FALSE]
head(expression.high)
dim(expression.high)
# 27 267
expression.mid = expression.share.signature[expression.share.signature$signature %like% "mid",,drop=FALSE]
expression.low = expression.share.signature[expression.share.signature$signature %like% "low",,drop=FALSE]
# signature.high
expression.high.p = apply(expression.share.signature[1:(ncol(expression.share.signature)-1)], 2, function(x) signif(t.test(x[1:nrow(expression.high)], x[(nrow(expression.high)+1):nrow(expression.share.signature)])$p.value,5))
head(expression.high.p)
length(expression.high.p)
# 266
expression.high.q = signif(p.adjust(expression.high.p, "BH"),5)
head(expression.high.q)
length(expression.high.q)
# 266
expression.high.mean1 = apply(expression.share.signature[1:(ncol(expression.share.signature)-1)], 2, function(x) signif(mean(na.omit(x[1:nrow(expression.high)])), 5))
expression.high.mean2 = apply(expression.share.signature[1:(ncol(expression.share.signature)-1)], 2, function(x) signif(mean(na.omit(x[(nrow(expression.high)+1):nrow(expression.share.signature)])), 5))
expression.high.fc = apply(expression.share.signature[1:(ncol(expression.share.signature)-1)], 2, function(x) signif(mean(na.omit(x[1:nrow(expression.high)])) / mean(na.omit(x[(nrow(expression.high)+1):nrow(expression.share.signature)])), 5))
head(expression.high.fc)
length(expression.high.fc)
# 266
expression.high.deg = data.frame(expression.high.mean1, expression.high.mean2, expression.high.fc, expression.high.p, expression.high.q, row.names=names(expression.high.fc))
colnames(expression.high.deg) = c("expression.high", "expression.other", "fc.high2other", "pvalue", "qvalue")
head(expression.high.deg)
dim(expression.high.deg)
# 4338 5
# write.csv(expression.high.deg, paste0("expression/dep_", signature.name, "_hml", cutoff.percentile, "_expression.high.deg.csv"), quote=TRUE)
# signature.low
expression.low.p = apply(expression.share.signature[1:(ncol(expression.share.signature)-1)], 2, function(x) signif(t.test(x[1:(nrow(expression.share.signature)-nrow(expression.low))], x[(nrow(expression.share.signature)-nrow(expression.low)+1):nrow(expression.share.signature)])$p.value,5))
head(expression.low.p)
length(expression.low.p)
# 266
expression.low.q = signif(p.adjust(expression.low.p, "BH"),5)
head(expression.low.q)
length(expression.low.q)
# 266
expression.low.mean1 = apply(expression.share.signature[1:(ncol(expression.share.signature)-1)], 2, function(x) signif(mean(na.omit(x[(nrow(expression.share.signature)-nrow(expression.low)+1):nrow(expression.share.signature)])), 5))
expression.low.mean2 = apply(expression.share.signature[1:(ncol(expression.share.signature)-1)], 2, function(x) signif(mean(na.omit(x[1:(nrow(expression.share.signature)-nrow(expression.low))])), 5))
expression.low.fc = apply(expression.share.signature[1:(ncol(expression.share.signature)-1)], 2, function(x) signif(mean(na.omit(x[(nrow(expression.share.signature)-nrow(expression.low)+1):nrow(expression.share.signature)])) / mean(na.omit(x[1:(nrow(expression.share.signature)-nrow(expression.low))])), 5))
head(expression.low.fc)
length(expression.low.fc)
# 266
expression.low.deg = data.frame(expression.low.mean1, expression.low.mean2, expression.low.fc, expression.low.p, expression.low.q, row.names=names(expression.low.fc))
colnames(expression.low.deg) = c("expression.low", "expression.other", "fc.low2other", "pvalue", "qvalue")
head(expression.low.deg)
dim(expression.low.deg)
# 4338 5
# write.csv(expression.low.deg, paste0("expression/dep_", signature.name, "_hml", cutoff.percentile, "_expression.low.deg.csv"), quote=TRUE)
# expression.high.deg = read.csv(paste0("expression/dep_", signature.name, "_hml", cutoff.percentile, "_expression.high.deg.csv"), header=TRUE, row.names=1)
# expression.low.deg = read.csv(paste0("expression/dep_", signature.name, "_hml", cutoff.percentile, "_expression.low.deg.csv"), header=TRUE, row.names=1)
# cutoff.qvalue = 0.1
# cutoff.fc = 2
set.seed(42)
p1 <- ggplot(data = expression.high.deg, mapping = aes(x = log(fc.high2other, 2), y = (-1)*log(qvalue, 10))) +
geom_point(size=0.5, color= ifelse(expression.high.deg$qvalue < cutoff.qvalue & expression.high.deg$fc.high2other > cutoff.fc, "red", ifelse(expression.high.deg$qvalue < cutoff.qvalue & expression.high.deg$fc.high2other < 1/cutoff.fc, "blue", "grey60")))+
# xlim(-1,1) +
# ylim(0,4) +
geom_hline(yintercept = (-1)*log(cutoff.qvalue, 10), linetype="dashed", colour="grey30", size=0.2) +
geom_vline(xintercept = log(cutoff.fc,2), linetype="dashed", colour="grey30", size=0.2) +
geom_vline(xintercept = (-1)*log(cutoff.fc,2), linetype="dashed", colour="grey30", size=0.2) +
annotate("text", x=min(log(expression.high.deg$fc.high2other[is.finite(expression.high.deg$fc.high2other) & expression.high.deg$fc.high2other > 0], 2))*0.9, y=max(na.omit((-1)*log(expression.low.deg$qvalue, 10)), na.omit((-1)*log(expression.high.deg$qvalue, 10)))*1.1, parse=FALSE, label = paste0("Signature.high cell lines: ", nrow(expression.share.signature.high)), color = "red", hjust = 0) +
# geom_label_repel(aes(label=ifelse(expression.high.deg$qvalue < (cutoff.qvalue) & abs(log(expression.high.deg$fc.high2other,2)) > log(cutoff.fc,2), as.character(rownames(expression.high.deg)), "")), size = 2, color = ifelse(expression.high.deg$fc.high2other < 0, "blue", "red"), segment.size=0.2) +
labs(x="Expression fold change (log2)", y="-log10(q value)", title=paste0("Signature [", signature.name, "] High vs. others"))
p1 <- p1 + rremove("legend") + theme_classic()
# p1
p2 <- ggplot(data = expression.low.deg, mapping = aes(x = log(fc.low2other, 2), y = (-1)*log(qvalue, 10))) +
geom_point(size=0.5, color= ifelse(expression.low.deg$qvalue < cutoff.qvalue & expression.low.deg$fc.low2other > cutoff.fc, "red", ifelse(expression.low.deg$qvalue < cutoff.qvalue & expression.low.deg$fc.low2other < 1/cutoff.fc, "blue", "grey60")))+
# xlim(-1,1) +
# ylim(0,4) +
geom_hline(yintercept = (-1)*log(cutoff.qvalue, 10), linetype="dashed", colour="grey30", size=0.2) +
geom_vline(xintercept = log(cutoff.fc,2), linetype="dashed", colour="grey30", size=0.2) +
geom_vline(xintercept = (-1)*log(cutoff.fc,2), linetype="dashed", colour="grey30", size=0.2) +
annotate("text", x=min(log(expression.low.deg$fc.low2other[is.finite(expression.low.deg$fc.low2other) & expression.low.deg$fc.low2other > 0], 2))*0.9, y=max(na.omit((-1)*log(expression.low.deg$qvalue, 10)), na.omit((-1)*log(expression.high.deg$qvalue, 10)))*1.1, parse=FALSE, label = paste0("Signature.low cell lines: ", nrow(expression.share.signature.low)), color = "red", hjust = 0) +
# geom_label_repel(aes(label=ifelse(expression.low.deg$qvalue < (cutoff.qvalue) & abs(log(expression.low.deg$fc.low2other,2)) > log(cutoff.fc,2), as.character(rownames(expression.low.deg)), "")), size = 2, color = ifelse(expression.low.deg$fc.low2other < 0, "blue", "red"), segment.size=0.2) +
labs(x="Expression fold change (log2)", y="-log10(q value)", title=paste0("Signature [", signature.name, "] Low vs. others"))
p2 <- p2 + rremove("legend") + theme_classic()
# p2
# Arranging the plot using cowplot
p = suppressWarnings(plot_grid(p1, p2, ncol = 2, align = "hv", rel_widths = c(1,1), rel_heights = c(1,1)))
# p <- ggplotGrob(p)
return(p)
}
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