ggsegRIO

email title: "Script for ggsegChen" - Hao (outlook mail)

Dec 7th 2020

Files stored on server

/space/chen-syn01/1/data/cinliu/plots/ggseg_brain_plots/ggsegRIO_12072020

scp -r /Users/nini/Desktop/2021lab/from_onedrive/plots/ggseg_brain_plots cinliu@137.110.172.99:/space/chen-syn01/1/data/cinliu/plots/ggseg_brain_plots/ggsegRIO_12072020

ggseg_update2_nini.R

rm(list=ls())
setwd('/Users/nini/Desktop/2020lab/carolina/ggseg_update/')library(ggsegChen)library(ggseg)library(dplyr)library(extrafont)
#change path to your dir where rg_forggsegChen.csv ispath='/Users/nini/Desktop/2020lab/carolina/ggseg/'all<-read.csv(file=paste0(path,"rg_forggsegChen_update.csv")) #fixed name spacing issue
#create four different files from R to generate four different sets of brain maps belowglob_area_area<-all[1:12,3:4]glob_area_thick<-all[13:24,3:4]glob_thick_area<-all[37:48,3:4]glob_thick_thick<-all[25:36,3:4]
# Plot 1: glob_area_area (rg between global area and regional area) - Doneb <- c(0.7,0.93)glob_area_area %>% ggseg(atlas = "chenAr", hemisphere="right", mapping = aes(fill = as.numeric(rg)), position = "stacked") + scale_fill_gradientn(limits = c(0.7,0.93), colours=c("magenta","magenta1","magenta2","magenta3","magenta4"),na.value = "transparent", breaks=b,labels=format(b)) + labs(title = "Global area & regional area") + theme(legend.position = "bottom", plot.title = element_text(vjust = -3), text = element_text(size = 7.5, family= "Arial"))ggsave("Rg between Global area and regional area.png", width = 6, height = 2)

# Plot 2: glob_area_thick (rg between global area and regional thickness)b <- c(-0.6,-0.1)glob_area_thick %>% ggseg(atlas = "chenTh", hemisphere="right",mapping = aes(fill = as.numeric(rg)), position = "stacked") + scale_fill_gradientn(limits = c(-0.6,-0.1), colours=c("blue4","blue3","#4040FF","#6060FF"),na.value = "transparent", breaks=b,labels=format(b)) + labs(title = "Global area & regional thickness") + theme(legend.position = "bottom", plot.title = element_text(vjust = -3), text = element_text(size = 7.5, family= "Arial"))ggsave("Rg between Global area and regional thickness.png", width = 6, height = 2)
# Plot 3: glob_thick_area (rg between global thickness and regional area) - Doneb <- c(-0.6,-0.1)glob_thick_area %>% ggseg(atlas = "chenAr",hemisphere="right", mapping = aes(fill = as.numeric(rg)), position = "stacked") + scale_fill_gradientn(limits = c(-0.6,-0.1), colours=c("blue4","blue3","#4040FF","#6060FF"),na.value = "transparent", breaks=b,labels=format(b)) + labs(title = "Global thickness & regional area") + theme(legend.position = "bottom", plot.title = element_text(vjust = -3), text = element_text(size = 7.5, family= "Arial")) # guides(fill = guide_legend(ncol = 4))ggsave("Rg between Global thickness and regional area.png", width = 6, height = 2)
# Plot 4: glob_thick_thick (rg between global thickness and regional thickness)b <- c(0.7,0.93)glob_thick_thick %>% ggseg(atlas = "chenTh",hemisphere="right", mapping = aes(fill = as.numeric(rg)), position = "stacked") + scale_fill_gradientn(limits = c(0.7,0.93), colours=c("magenta","magenta1","magenta2","magenta3","magenta4"),na.value = "transparent", breaks=b,labels=format(b)) + labs(title = "Global thickness & regional thickness",line = -2) + theme(legend.position = "bottom", plot.title = element_text(vjust = -3), text = element_text(size = 7.5, family= "Arial")) #guides(fill = guide_legend(ncol = 4))ggsave("Rg between Global thickness and regional thickness.png", width = 6, height = 2)

For help on how to make ggseg plots see Brainplot_p_global

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