From fb376db9f32cb508741c9354841814041519a293 Mon Sep 17 00:00:00 2001 From: Wei Feng Ma Date: Mon, 31 Dec 2018 19:19:23 -0500 Subject: [PATCH] minor changes in color scale also changed the functions used to retrieve data to remove the requirement of a subfolder in the working directory. --- [FINAL] NADPH-GenePanels-HEATMAP.R | 9 +- ...] NOX4-EMT-HEATMAP_UnsupervisedClustered.R | 161 ++++-------------- 2 files changed, 34 insertions(+), 136 deletions(-) diff --git a/[FINAL] NADPH-GenePanels-HEATMAP.R b/[FINAL] NADPH-GenePanels-HEATMAP.R index 1640754..040c785 100644 --- a/[FINAL] NADPH-GenePanels-HEATMAP.R +++ b/[FINAL] NADPH-GenePanels-HEATMAP.R @@ -465,12 +465,11 @@ dl.RNA.select <- function(y) { # CNV_SNP = T, # copy number alterantion in germline cells # Methylation = T, # methylation provided by array platform # RPPA = T, # reverse phase protein array expression - RNAseq2_Gene_Norm = TRUE, + RNASeq2GeneNorm = T, + RNAseq2Norm = "normalized_count", # normalized count - fileSizeLimit = 99999, # getUUIDs = T, - destdir = "FireHose Data", - forceDownload = F + forceDownload = T ) edit <- gather(rownames_to_column(as.data.frame(getData(set, type = "RNASeq2GeneNorm")), var = "Gene.Symbol"), key = "Patient.ID", value = "mRNA.Value", -Gene.Symbol) # extract RNAseq, transform row name as a colmn, then transform into long form @@ -757,7 +756,7 @@ calc.rho.unclustered.no_p53 <- pretty.order.cols = TRUE, left.label.text.alignment = "right", bottom.label.text.alignment = "right", - heat.pal = c("turquoise", "white", "violetred1"), + heat.pal = c("deepskyblue3", "white", "red2"), heat.lim = c(-1,1), legend.breaks = c(-0.8,0,0.8) ) diff --git a/[FINAL] NOX4-EMT-HEATMAP_UnsupervisedClustered.R b/[FINAL] NOX4-EMT-HEATMAP_UnsupervisedClustered.R index 4bbcbe8..ed017d2 100644 --- a/[FINAL] NOX4-EMT-HEATMAP_UnsupervisedClustered.R +++ b/[FINAL] NOX4-EMT-HEATMAP_UnsupervisedClustered.R @@ -11,8 +11,9 @@ library(tibble) library(ggforce) library(superheat) # custom install from github, -# install.packages("devtools") -# devtools::install_github("rlbarter/superheat") +# source("https://install-github.me/r-lib/callr") # install callr dependency for devtools +# install.packages("devtools") # install devtools +# devtools::install_github("rlbarter/superheat") # use devtools to install superheat library(dplyr) ### Set Working Directory PLEASE ADJUST TO YOUR COMPUTER ---- @@ -462,12 +463,11 @@ dl.RNA.select <- function(y) { # CNV_SNP = T, # copy number alterantion in germline cells # Methylation = T, # methylation provided by array platform # RPPA = T, # reverse phase protein array expression - RNAseq2_Gene_Norm = TRUE, + RNASeq2GeneNorm = T, + RNAseq2Norm = "normalized_count", # normalized count - fileSizeLimit = 99999, # getUUIDs = T, - destdir = "FireHose Data", - forceDownload = F + forceDownload = T ) edit <- gather(rownames_to_column(as.data.frame(getData(set, type = "RNASeq2GeneNorm")), var = "Gene.Symbol"), key = "Patient.ID", value = "mRNA.Value", -Gene.Symbol) # extract RNAseq, transform row name as a colmn, then transform into long form @@ -719,7 +719,7 @@ calc.rho.unclustered.no_p53 <- pretty.order.cols = TRUE, left.label.text.alignment = "right", bottom.label.text.alignment = "right", - heat.pal = c("turquoise", "white", "violetred1"), + heat.pal = c("deepskyblue3", "white", "red2"), heat.lim = c(-0.8,0.8)) dev.off() @@ -762,7 +762,7 @@ head(Pan.final) #### NADPHoxidase correlations to genepanels faceted by p53 ---- -Make.heatmap.p53 <- function(NOX.master = "NOX4", gene_list_master = EMT.SAbiosci.genes, dpi = 600, wid = 9, hei = 4) { +Make.heatmap.p53 <- function(NOX.master = "NOX4", BLsize = 1, gene_list_master = EMT.SAbiosci.genes, dpi = 600, wid = 9, hei = 4) { filter.nox <- function(NOX = NOX.master, mutation, gene_list = gene_list_master) { # outputs the rho of the specificed NOX to the specified genes in the specific p53 mutant group @@ -847,7 +847,7 @@ Make.heatmap.p53 <- function(NOX.master = "NOX4", gene_list_master = EMT.SAbiosc superheat( combined.rho.final, bottom.label.text.angle = 90, - bottom.label.text.size = 3, + bottom.label.text.size = 4, scale = F, grid.hline.col = "white", grid.vline.col = "white", @@ -857,7 +857,8 @@ Make.heatmap.p53 <- function(NOX.master = "NOX4", gene_list_master = EMT.SAbiosc pretty.order.cols = T, left.label.text.alignment = "right", bottom.label.text.alignment = "right", - heat.pal = c("turquoise", "white", "violetred1"), + bottom.label.size = BLsize, + heat.pal = c("deepskyblue3", "white", "red2"), heat.lim = c(-1,1), legend.breaks = c(-0.8,0,0.8)) @@ -870,7 +871,7 @@ Make.heatmap.p53 <- function(NOX.master = "NOX4", gene_list_master = EMT.SAbiosc superheat( combined.rho.final, bottom.label.text.angle = 90, - bottom.label.text.size = 3, + bottom.label.text.size = 4, scale = F, grid.hline.col = "white", grid.vline.col = "white", @@ -880,132 +881,22 @@ Make.heatmap.p53 <- function(NOX.master = "NOX4", gene_list_master = EMT.SAbiosc row.dendrogram = T, left.label.text.alignment = "right", bottom.label.text.alignment = "right", - heat.pal = c("turquoise", "white", "violetred1"), - heat.lim = c(-1,1), - legend.breaks = c(-0.8,0,0.8)) - - - dev.off() -} -Make.heatmap.p53.n <- function(NOX.master = "NOX4", gene_list_master = EMT.SAbiosci.genes, dpi = 600, wid = 9, hei = 4) { - # this function will attach a yplot with n to the heatmap - filter.nox <- function(NOX = NOX.master, mutation, gene_list = gene_list_master) { - # outputs the rho of the specificed NOX to the specified genes in the specific p53 mutant group - # I chosed not to use piping operator on purpose to examine each df created - df.0 <- - Pan.final[Pan.final$P53.Mutation %in% mutation,] # isolate an individual mutant - df.1 <- select(df.0, -Case.Study) # removes case study column - df.2 <- unique(df.1, nmax = 2) - df.3 <- - spread(data = df.2, - key = Gene.Symbol, - value = mRNA.Value) # change to wide format to make matrix - rownames(df.3) <- df.3$Patient.ID - df.4 <- select(df.3, -Patient.ID, -P53.Mutation) - df.cor <- - cor(df.4, method = "spearman", use = "pairwise.complete.obs") - df.5 <- t(as.matrix(df.cor[NOX, ])) - rownames(df.5) <- mutation - - # so now df.5 is the defined row with rho values - - df.6 <- df.5[, gene_list] - df.6 - } - - R175H <- filter.nox(mutation = "R175H") - R248Q <- filter.nox(mutation = "R248Q") - R273H <- filter.nox(mutation = "R273H") - R273C <- filter.nox(mutation = "R273C") - R248W <- filter.nox(mutation = "R248W") - Y220C <- filter.nox(mutation = "Y220C") - R249S <- filter.nox(mutation = "R249S") - G245D <- filter.nox(mutation = "G245D") - R273C <- filter.nox(mutation = "R273C") - R248Q <- filter.nox(mutation = "R248Q") - H179R <- filter.nox(mutation = "H179R") - R282W <- filter.nox(mutation = "R282W") - V157F <- filter.nox(mutation = "V157F") - H193R <- filter.nox(mutation = "H193R") - R158L <- filter.nox(mutation = "R158L") - R273L <- filter.nox(mutation = "R273L") - R158L <- filter.nox(mutation = "R158L") - H179R <- filter.nox(mutation = "H179R") - G245S <- filter.nox(mutation = "G245S") - WT <- filter.nox(mutation = "WT") - - all_grouping <- rbind( - R175H, - R248Q, - R273H, - R273C, - R248W, - Y220C, - R249S, - G245D, - R273C, - R248Q, - H179R, - R282W, - V157F, - H193R, - R158L, - R273L, - # G248S, # very few of these - R158L, - # C175F, # very few of these - H179R, - G245S, - WT - ) - - combined.rho <- unique(as.data.frame(all_grouping)) - combined.n <- Pan.final %>% - group_by(P53.Mutation) %>% - summarise(count = (length(P53.Mutation)/138)) # 138 genes per person - - # noxes tha should no tbe included into the heatmap - noxes.vector <- c("NOX4", "NOX1", "CYBB", "CYBA", "NOX3", "NOX5", "DUOX1", "DUOX2") # specified order - - combined.rho.final <- combined.rho[, !colnames(combined.rho) %in% noxes.vector] - - png(paste(deparse(substitute(gene_list_master)), NOX.master, # deparse(substitute()) calls the name of the df as character string - "_byp53_n.png"), width = wid, height = hei, units = 'in', res = dpi) - - superheat( - combined.rho.final, - bottom.label.text.angle = 90, - bottom.label.text.size = 3, - scale = F, - grid.hline.col = "white", - grid.vline.col = "white", - grid.hline.size = 1, - grid.vline.size = 1, - pretty.order.rows = T, # unspervised clustering for rows, t= true - pretty.order.cols = T, - left.label.text.alignment = "right", - bottom.label.text.alignment = "right", - heat.pal = c("turquoise", "white", "violetred1"), + bottom.label.size = BLsize, + heat.pal = c("deepskyblue3", "white", "red2"), heat.lim = c(-1,1), - yr = (combined.n$count), - yr.axis.name = "n of samples", - yr.plot.type = "bar", legend.breaks = c(-0.8,0,0.8)) dev.off() - - } # for NOX4 -Make.heatmap.p53(NOX.master = "NOX4", gene_list_master = EMT.SAbiosci.genes, dpi = 900, wid = 10.5, hei = 6.5) -Make.heatmap.p53.n(NOX.master = "NOX4", gene_list_master = EMT.SAbiosci.genes, dpi = 900, wid = 10.5, hei = 6.5) +Make.heatmap.p53(NOX.master = "NOX4", BLsize = 0.401, gene_list_master = EMT.SAbiosci.genes, dpi = 900, wid = 10.5, hei = 7) #### NADPHoxidase correlations to genepanels faceted by WT OR MUT (generalized) ---- -Make.heatmap.p53.generalized <- function(NOX.master = "NOX4", gene_list_master = EMT.SAbiosci.genes, dpi = 600, wid = 9, hei = 6.5) { +Make.heatmap.p53.generalized <- function(NOX.master = "NOX4", BLsize = 0.401, gene_list_master = EMT.SAbiosci.genes, dpi = 600, wid = 9, hei = 6.5) { filter.nox.WT <- function(NOX = NOX.master, mutation, gene_list = gene_list_master) { # outputs the rho of the specificed NOX to the specified genes in the specific p53 mutant group @@ -1109,7 +1000,7 @@ Make.heatmap.p53.generalized <- function(NOX.master = "NOX4", gene_list_master = superheat( combined.rho.final, bottom.label.text.angle = 90, - bottom.label.text.size = 3, + bottom.label.text.size = 4, scale = F, grid.hline.col = "white", grid.vline.col = "white", @@ -1119,7 +1010,8 @@ Make.heatmap.p53.generalized <- function(NOX.master = "NOX4", gene_list_master = pretty.order.cols = T, left.label.text.alignment = "right", bottom.label.text.alignment = "right", - heat.pal = c("turquoise", "white", "violetred1"), + bottom.label.size = BLsize, + heat.pal = c("deepskyblue3", "white", "red2"), heat.lim = c(-1,1), legend = F) @@ -1134,7 +1026,7 @@ Make.heatmap.p53.generalized <- function(NOX.master = "NOX4", gene_list_master = superheat( combined.rho.final, bottom.label.text.angle = 90, - bottom.label.text.size = 3, + bottom.label.text.size = 4, scale = F, grid.hline.col = "white", grid.vline.col = "white", @@ -1144,7 +1036,8 @@ Make.heatmap.p53.generalized <- function(NOX.master = "NOX4", gene_list_master = row.dendrogram = F, left.label.text.alignment = "right", bottom.label.text.alignment = "right", - heat.pal = c("turquoise", "white", "violetred1"), + bottom.label.size = BLsize, + heat.pal = c("deepskyblue3", "white", "red2"), heat.lim = c(-1,1), legend = F) @@ -1158,7 +1051,7 @@ Make.heatmap.p53.generalized <- function(NOX.master = "NOX4", gene_list_master = superheat( combined.rho.final, bottom.label.text.angle = 90, - bottom.label.text.size = 3, + bottom.label.text.size = 4, scale = F, grid.hline.col = "white", grid.vline.col = "white", @@ -1171,7 +1064,8 @@ Make.heatmap.p53.generalized <- function(NOX.master = "NOX4", gene_list_master = X.text.col = "grey", left.label.text.alignment = "right", bottom.label.text.alignment = "right", - heat.pal = c("turquoise", "white", "violetred1"), + bottom.label.size = BLsize, + heat.pal = c("deepskyblue3", "white", "red2"), heat.lim = c(-1,1), legend = F) @@ -1183,3 +1077,8 @@ Make.heatmap.p53.generalized <- function(NOX.master = "NOX4", gene_list_master = # for NOX4 Make.heatmap.p53.generalized(NOX.master = "NOX4", gene_list_master = EMT.SAbiosci.genes, dpi = 900, wid = 10.5, hei = 6.5) +CPCOLS <- c("#2398EB", "#33a02c", "#e31a1c") + +ggplot(iris, aes(Sepal.Length, Petal.Length)) + + geom_point(aes(col = Species)) + + scale_colour_manual(values = CPCOLS) \ No newline at end of file