Embedded Files
location on server: /space/chen-syn01/1/data/cinliu/plots/barplots/barplot_with_star
Initial instructions:
Just to give some context, these are summary tables comparing the beta estimates (a proxy for effect sizes and direction of effect in GWAS) between our discovery dataset and a replication dataset for the 24 brain imaging phenotypes of interest.Initial instructions:
I would want a bar plot for each file, where the y-axis is "Region", the x-axis is "r", and the bars are coloured by "Measure". The bars should be sorted from largest to smallest r-value.
Then for the "posbetas_" and "negbetas_*" files, I would want to indicate somehow the bars that have a pval<0.0025, and those with a pval<0.05. For instance, maybe two asterisks marking pval<0.0025, and one asterisk for pval<0.05? This wouldn't apply for the "allbetas_*" file because they are all significantly correlated.
What I did:
install ggplot2 and ggsignif
input the data
make geom_bar() to make a basic bar plot
y= r
x= region reordered by r
fill = measurement
use coord_flip() to make sure the x and y axis is reversed
specify color (she wants blue and dark blue)
Adding significant * to the plot - you basicall add a new column to the data, this new column will literly add a * or ** in that collumn if the value is significant.
In the example here dataP$pval less then 0.05 will get one star, less then 0.0025 will get 2 stars. We then pull them out as subset data.
#stars
dataP$star <- ""
dataP$star[dataP$pval<0.05] <- "*"
dataP$star[dataP$pval<0.0025] <- "**"
pfivesub <- subset.data.frame(dataP,star == "*")
ptwosub <- subset.data.frame(dataP,star == "**")
And then once you have then stars given. Label them in the plot
geom_text(data = fivesub, label = "*", size =15) +
geom_text(data = twosub, label = "**", size =15) +
output with ggsave
Full bar_plots_carolina.R:
Full bar_plots_carolina.R:
#setup rm(list=ls())library(ggplot2)library(ggsignif)
setwd("/Users/niniliu/Desktop/2020lab/carolina plots") #updateDDir='/Users/niniliu/Desktop/2020lab/carolina plots/' #update
dataA = read.table(paste0(DDir,'allbetas_ABCD_UKB_betacorr_newlab.txt'), h=T) #updatedataP = read.table(paste0(DDir,'posbetas_ABCD_UKB_betacorr_newlab.txt'), h=T)dataN = read.table(paste0(DDir,'negbetas_ABCD_UKB_betacorr_newlab.txt'), h=T)
#allbetas plot Aplot <- ggplot(dataA, aes(fill=Measure, y=r, x= reorder(Region, r))) + geom_bar(position="dodge",stat = "identity",width=0.7)+ coord_flip()+ labs( x= "Region")+ scale_fill_manual("Measurement", values = c('area' = 'royalblue', 'thickness' = "deepskyblue"))+ theme(axis.title.x= element_text(size = 27), axis.text.x= element_text(size = 24), axis.title.y = element_text(size = 27), axis.text.y = element_text(size = 24), legend.title = element_text( size = 27), legend.text = element_text(size = 24), axis.ticks.length=unit(.25, "cm"))Aplotggsave(filename = "AllBetas.png", Aplot, width = 13.5, height = 15, dpi = 300, pointsize = 24, units = "in")
#stars dataP$star <- ""dataP$star[dataP$pval<0.05] <- "*"dataP$star[dataP$pval<0.0025] <- "**"
pfivesub <- subset.data.frame(dataP,star == "*")ptwosub <- subset.data.frame(dataP,star == "**")
Pplot <- ggplot(dataP, aes(fill=Measure, y=r, x= reorder(Region, r))) + geom_bar(position="dodge",stat = "identity" ,width=0.7)+ coord_flip() + labs( x= "Region")+ scale_fill_manual("Measurement", values = c('area' = 'royalblue', 'thickness' = "deepskyblue"))+geom_text(data = pfivesub, label = "*", size =15) + geom_text(data = ptwosub, label = "**", size =15) + theme(axis.title.x= element_text(size = 26), axis.text.x= element_text(size = 24), axis.title.y = element_text(size = 26), axis.text.y = element_text(size = 24), legend.title = element_text( size = 26), legend.text = element_text(size = 24), axis.ticks.length=unit(.25, "cm"))Pplotggsave(filename = "PosBetas.png", Pplot, width = 13.5, height = 15, dpi = 300, pointsize = 24, units = "in")
#nplotdataN$star <- ""dataN$star[dataN$pval <= 0.05] <- "*"dataN$star[dataN$pval <= 0.0025] <- "**"
fivesub <- subset.data.frame(dataN,star == "*")twosub <- subset.data.frame(dataN,star == "**")####testign ploot
Nplot <- ggplot(dataN, aes(fill=Measure, y=r, x= reorder(Region, r))) + geom_bar(position="dodge",stat = "identity" ,width=0.7)+ coord_flip() + labs( x= "Region")+ scale_fill_manual("Measurement", values = c('area' = 'royalblue', 'thickness' = "deepskyblue")) + geom_text(data = fivesub, label = "*", size =15) + geom_text(data = twosub, label = "**", size =15) + theme(axis.title.x= element_text(size = 26), axis.text.x= element_text(size = 24), axis.title.y = element_text(size = 26), axis.text.y = element_text(size = 24), legend.title = element_text( size = 26), legend.text = element_text(size = 24), axis.ticks.length=unit(.25, "cm"))
Nplotggsave(filename = "NegBetas.png", Nplot, width = 13.5, height = 15, dpi = 300, pointsize = 24, units = "in")
setwd("/Users/niniliu/Desktop/2020lab/carolina plots") #updateDDir='/Users/niniliu/Desktop/2020lab/carolina plots/' #update
dataA = read.table(paste0(DDir,'allbetas_ABCD_UKB_betacorr_newlab.txt'), h=T) #updatedataP = read.table(paste0(DDir,'posbetas_ABCD_UKB_betacorr_newlab.txt'), h=T)dataN = read.table(paste0(DDir,'negbetas_ABCD_UKB_betacorr_newlab.txt'), h=T)
#allbetas plot Aplot <- ggplot(dataA, aes(fill=Measure, y=r, x= reorder(Region, r))) + geom_bar(position="dodge",stat = "identity",width=0.7)+ coord_flip()+ labs( x= "Region")+ scale_fill_manual("Measurement", values = c('area' = 'royalblue', 'thickness' = "deepskyblue"))+ theme(axis.title.x= element_text(size = 27), axis.text.x= element_text(size = 24), axis.title.y = element_text(size = 27), axis.text.y = element_text(size = 24), legend.title = element_text( size = 27), legend.text = element_text(size = 24), axis.ticks.length=unit(.25, "cm"))Aplotggsave(filename = "AllBetas.png", Aplot, width = 13.5, height = 15, dpi = 300, pointsize = 24, units = "in")
#stars dataP$star <- ""dataP$star[dataP$pval<0.05] <- "*"dataP$star[dataP$pval<0.0025] <- "**"
pfivesub <- subset.data.frame(dataP,star == "*")ptwosub <- subset.data.frame(dataP,star == "**")
Pplot <- ggplot(dataP, aes(fill=Measure, y=r, x= reorder(Region, r))) + geom_bar(position="dodge",stat = "identity" ,width=0.7)+ coord_flip() + labs( x= "Region")+ scale_fill_manual("Measurement", values = c('area' = 'royalblue', 'thickness' = "deepskyblue"))+geom_text(data = pfivesub, label = "*", size =15) + geom_text(data = ptwosub, label = "**", size =15) + theme(axis.title.x= element_text(size = 26), axis.text.x= element_text(size = 24), axis.title.y = element_text(size = 26), axis.text.y = element_text(size = 24), legend.title = element_text( size = 26), legend.text = element_text(size = 24), axis.ticks.length=unit(.25, "cm"))Pplotggsave(filename = "PosBetas.png", Pplot, width = 13.5, height = 15, dpi = 300, pointsize = 24, units = "in")
#nplotdataN$star <- ""dataN$star[dataN$pval <= 0.05] <- "*"dataN$star[dataN$pval <= 0.0025] <- "**"
fivesub <- subset.data.frame(dataN,star == "*")twosub <- subset.data.frame(dataN,star == "**")####testign ploot
Nplot <- ggplot(dataN, aes(fill=Measure, y=r, x= reorder(Region, r))) + geom_bar(position="dodge",stat = "identity" ,width=0.7)+ coord_flip() + labs( x= "Region")+ scale_fill_manual("Measurement", values = c('area' = 'royalblue', 'thickness' = "deepskyblue")) + geom_text(data = fivesub, label = "*", size =15) + geom_text(data = twosub, label = "**", size =15) + theme(axis.title.x= element_text(size = 26), axis.text.x= element_text(size = 24), axis.title.y = element_text(size = 26), axis.text.y = element_text(size = 24), legend.title = element_text( size = 26), legend.text = element_text(size = 24), axis.ticks.length=unit(.25, "cm"))
Nplotggsave(filename = "NegBetas.png", Nplot, width = 13.5, height = 15, dpi = 300, pointsize = 24, units = "in")
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