Location on server: /space/chen-syn01/1/data/cinliu/plots/fig5a_fromJenny
email title 'Fw:plotting' Sep 3rd 2020
Embedded Files
figure 5a adjustments
initial instructions:
Could you use Jenny's data matrix to improve font size/bold for figure 5a?
Additionally, please use black circle + dot means < 0.0025, dot means > 0.0025 but < 0.01? I really like that plot you made https://drive.google.com/drive/folders/1RrG50iRNodROSDDHQxczisLYM0V3k4yH
Goal
Goal
Change a heatmap to ggplot (geom_point)
Before:
After:
Original ggHeat code (by Jenny)
figure5a_script.R
devtools::install_github("linxihui/NNLM")
library(swne)library(cowplot)
setwd("/Users/niniliu/Desktop/2020lab/ch-email/figure5a/")load('figure5a_mat.RData')# Note: the matrix is named as 'combined.heatmap.mat.pval.rev'pval.df <- FlattenMatrix(combined.heatmap.mat.pval.rev)pval.df <- subset(pval.df, (value < 0.01) & (value > 0.0025))
sig.pval.df <- subset(pval.df, value < 0.0025)
plot.df <- rbind(pval.df, sig.pval.df)
# Make log10 heatmappdf("figure5a.pdf", width = 12, height = 11)ggHeat(-log10(combined.heatmap.mat.pval.rev), clustering = "none", x.lab.size = 10, y.lab.size = 11, heatscale = c(low="white", mid="white", high = "tomato"), legend.title = '-log10 Enrichment p-val') + geom_point(aes(x = colInd, y = rowInd, shape = "sig"), data = pval.df, show.legend = T) + geom_point(aes(x = colInd, y = rowInd, shape = "very sig"), data = sig.pval.df) + scale_size_area(guide = F) + scale_shape_manual(breaks = c("sig", "very sig"), values = c(1,16), labels = c(" 0.0025< p < 0.01 ", " p < 0.0025"))dev.off()
library(swne)library(cowplot)
setwd("/Users/niniliu/Desktop/2020lab/ch-email/figure5a/")load('figure5a_mat.RData')# Note: the matrix is named as 'combined.heatmap.mat.pval.rev'pval.df <- FlattenMatrix(combined.heatmap.mat.pval.rev)pval.df <- subset(pval.df, (value < 0.01) & (value > 0.0025))
sig.pval.df <- subset(pval.df, value < 0.0025)
plot.df <- rbind(pval.df, sig.pval.df)
# Make log10 heatmappdf("figure5a.pdf", width = 12, height = 11)ggHeat(-log10(combined.heatmap.mat.pval.rev), clustering = "none", x.lab.size = 10, y.lab.size = 11, heatscale = c(low="white", mid="white", high = "tomato"), legend.title = '-log10 Enrichment p-val') + geom_point(aes(x = colInd, y = rowInd, shape = "sig"), data = pval.df, show.legend = T) + geom_point(aes(x = colInd, y = rowInd, shape = "very sig"), data = sig.pval.df) + scale_size_area(guide = F) + scale_shape_manual(breaks = c("sig", "very sig"), values = c(1,16), labels = c(" 0.0025< p < 0.01 ", " p < 0.0025"))dev.off()
Modified using geom_point code
figure_5a_bold.R
rm(list=ls())library(ggplot2)library(gplots)library(reshape)library(tidyverse)
#firgure 5a setwd("/Users/niniliu/Desktop/2020lab/ch-email/figure5a")load('figure5a_mat.RData')
# Note: the matrix is named as 'combined.heatmap.mat.pval.rev'pval.df <- as.data.frame(combined.heatmap.mat.pval.rev)df.melt <- melt(myMat)
#dimnamesmyMat <- as.matrix(pval.df)names(dimnames(myMat)) <- c("Names.of.Rows", "")df.melt <- melt(myMat)
df.melt$neglog10 <- -log10(df.melt$value)
#########keep order row <- as.factor(rownames(pval.df))df.melt$Names.of.Rows <- ordered(df.melt$Names.of.Rows, levels = row)
c <- as.factor(colnames(pval.df))df.melt$Var.2 <- ordered(df.melt$Var.2, levels = c)
###x <- as.numeric(df.melt$value)class(x)
saveplot <- ggplot(df.melt, aes(Var.2,Names.of.Rows)) + geom_point(aes(fill=neglog10), colour= ifelse(x<0.0025, "black", "white"), shape=21, size=7) + labs( y="", x="", title="", fill= "-log10 Enrichment p-val")+ theme_bw()+ theme(panel.grid.major = element_blank(), panel.grid.minor = element_blank(), axis.text.x = element_text(angle = 90, hjust = 1, vjust=0.5, size = 16, face="bold"), axis.text.y = element_text(angle = 0,size=16, face="bold")) + scale_fill_gradient2(low = "white", high = "tomato")
Nplot <- saveplot + geom_point(data = df.melt[df.melt$value <0.01, ], aes(x=Var.2, y=Names.of.Rows),shape ="*", size=8)+ scale_shape_manual() ggsave(filename = "font16.png", Nplot, width = 13, height = 9.9, dpi = 300, units = "in")#manually add the ledgend for 'shape'
#firgure 5a setwd("/Users/niniliu/Desktop/2020lab/ch-email/figure5a")load('figure5a_mat.RData')
# Note: the matrix is named as 'combined.heatmap.mat.pval.rev'pval.df <- as.data.frame(combined.heatmap.mat.pval.rev)df.melt <- melt(myMat)
#dimnamesmyMat <- as.matrix(pval.df)names(dimnames(myMat)) <- c("Names.of.Rows", "")df.melt <- melt(myMat)
df.melt$neglog10 <- -log10(df.melt$value)
#########keep order row <- as.factor(rownames(pval.df))df.melt$Names.of.Rows <- ordered(df.melt$Names.of.Rows, levels = row)
c <- as.factor(colnames(pval.df))df.melt$Var.2 <- ordered(df.melt$Var.2, levels = c)
###x <- as.numeric(df.melt$value)class(x)
saveplot <- ggplot(df.melt, aes(Var.2,Names.of.Rows)) + geom_point(aes(fill=neglog10), colour= ifelse(x<0.0025, "black", "white"), shape=21, size=7) + labs( y="", x="", title="", fill= "-log10 Enrichment p-val")+ theme_bw()+ theme(panel.grid.major = element_blank(), panel.grid.minor = element_blank(), axis.text.x = element_text(angle = 90, hjust = 1, vjust=0.5, size = 16, face="bold"), axis.text.y = element_text(angle = 0,size=16, face="bold")) + scale_fill_gradient2(low = "white", high = "tomato")
Nplot <- saveplot + geom_point(data = df.melt[df.melt$value <0.01, ], aes(x=Var.2, y=Names.of.Rows),shape ="*", size=8)+ scale_shape_manual() ggsave(filename = "font16.png", Nplot, width = 13, height = 9.9, dpi = 300, units = "in")#manually add the ledgend for 'shape'
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