Brainmap for genomicSEM UKB2factor

email title: "Brainmaps for genomicSEM UKB2factor" - Chi Hua (outlook mail)

Feb 10th 2021

Location on server: /space/chen-syn01/1/data/cinliu/plots/UKB_2Factor_brainmap

Files used:

Sample plot (the rest are in the link):

Step 1: Basic set up

Use rm(list=ls()) to clear list in R so we have a new/clean enviroment to work with.

Set working directory with setwd() . This particular file we are saving it in the location '/Users/nini/Desktop/2021lab/CH/brainmap/'

#2 factor brain map rm(list=ls())
setwd('/Users/nini/Desktop/2021lab/CH/brainmap/')library(ggsegChen)library(ggseg)library(dplyr)library(readxl

Step 2: Input file and adjust

Input the file and change the region names so it matches with the region names of ggseg.

note: The ggseg package is very specific about the way the region name is labeled so make sure it is exactly the same as how ggseg names the regions and make sure there are no accidental space before or after the words.

Chenpheno_abbrev <- read.delim("~/Downloads/Chenpheno_abbrev.txt") Chenpheno_abbrev$Region
Chenpheno_abbrev$Region<- gsub("_area", "", Chenpheno_abbrev$Region)Chenpheno_abbrev$Region<- gsub("_thickness", "", Chenpheno_abbrev$Region)Chenpheno_abbrev[Chenpheno_abbrev$Region == "ventromedialoccipital",1] <- "ventromedial occipital"Chenpheno_abbrev[Chenpheno_abbrev$Region == "ventralfrontal",1] <- "ventral frontal"Chenpheno_abbrev[Chenpheno_abbrev$Region == "temporalpole",1] <- "temporal pole"Chenpheno_abbrev[Chenpheno_abbrev$Region == "superiorparietal",1] <- "superior parietal"Chenpheno_abbrev[Chenpheno_abbrev$Region == "motor_premotor_SMA",1] <- "motor-premotor-supplementary motor area"Chenpheno_abbrev[Chenpheno_abbrev$Region == "middletemporal",1] <- "middle temporal"Chenpheno_abbrev[Chenpheno_abbrev$Region == "medialtemporal",1] <- "medial temporal"Chenpheno_abbrev[Chenpheno_abbrev$Region == "medialprefrontal",1] <- "medial prefrontal"Chenpheno_abbrev[Chenpheno_abbrev$Region == "inferiorparietal",1] <- "inferior parietal"Chenpheno_abbrev[Chenpheno_abbrev$Region == "dorsolateralprefrontal",1] <- "dorsolateral prefrontal"Chenpheno_abbrev[Chenpheno_abbrev$Region == "superiortemporal",1] <- "superior temporal"Chenpheno_abbrev[Chenpheno_abbrev$Region == "parsopercularis",1] <- "pars opercularis,subcentral"Chenpheno_abbrev[Chenpheno_abbrev$Region == "inferiorparietal",1] <- "inferior parietal"Chenpheno_abbrev[Chenpheno_abbrev$Region == "dorsolateralprefrontal",1] <- "dorsolateral prefrontal"Chenpheno_abbrev[Chenpheno_abbrev$Region == "superiorparietal",1] <- "superior parietal"Chenpheno_abbrev[Chenpheno_abbrev$Region == "posterolateraltemporal",1] <- "posterolateral temporal"Chenpheno_abbrev[Chenpheno_abbrev$Region == "motorpremotor",1] <- "motor-premotor"Chenpheno_abbrev[Chenpheno_abbrev$Region == "dorsomedialfrontal",1] <- "dorsomedial frontal"Chenpheno_abbrev[Chenpheno_abbrev$Region == "anteromedialtemporal",1] <- "anteromedial temporal"

2facor_brainmap.R

#2 factor brain map rm(list=ls())
setwd('/Users/nini/Desktop/2021lab/CH/brainmap/')library(ggsegChen)library(ggseg)library(dplyr)library(readxl)
Chenpheno_abbrev <- read.delim("~/Downloads/Chenpheno_abbrev.txt") Chenpheno_abbrev$Region
Chenpheno_abbrev$Region<- gsub("_area", "", Chenpheno_abbrev$Region)Chenpheno_abbrev$Region<- gsub("_thickness", "", Chenpheno_abbrev$Region)Chenpheno_abbrev[Chenpheno_abbrev$Region == "ventromedialoccipital",1] <- "ventromedial occipital"Chenpheno_abbrev[Chenpheno_abbrev$Region == "ventralfrontal",1] <- "ventral frontal"Chenpheno_abbrev[Chenpheno_abbrev$Region == "temporalpole",1] <- "temporal pole"Chenpheno_abbrev[Chenpheno_abbrev$Region == "superiorparietal",1] <- "superior parietal"Chenpheno_abbrev[Chenpheno_abbrev$Region == "motor_premotor_SMA",1] <- "motor-premotor-supplementary motor area"Chenpheno_abbrev[Chenpheno_abbrev$Region == "middletemporal",1] <- "middle temporal"Chenpheno_abbrev[Chenpheno_abbrev$Region == "medialtemporal",1] <- "medial temporal"Chenpheno_abbrev[Chenpheno_abbrev$Region == "medialprefrontal",1] <- "medial prefrontal"Chenpheno_abbrev[Chenpheno_abbrev$Region == "inferiorparietal",1] <- "inferior parietal"Chenpheno_abbrev[Chenpheno_abbrev$Region == "dorsolateralprefrontal",1] <- "dorsolateral prefrontal"Chenpheno_abbrev[Chenpheno_abbrev$Region == "superiortemporal",1] <- "superior temporal"Chenpheno_abbrev[Chenpheno_abbrev$Region == "parsopercularis",1] <- "pars opercularis,subcentral"Chenpheno_abbrev[Chenpheno_abbrev$Region == "inferiorparietal",1] <- "inferior parietal"Chenpheno_abbrev[Chenpheno_abbrev$Region == "dorsolateralprefrontal",1] <- "dorsolateral prefrontal"Chenpheno_abbrev[Chenpheno_abbrev$Region == "superiorparietal",1] <- "superior parietal"Chenpheno_abbrev[Chenpheno_abbrev$Region == "posterolateraltemporal",1] <- "posterolateral temporal"Chenpheno_abbrev[Chenpheno_abbrev$Region == "motorpremotor",1] <- "motor-premotor"Chenpheno_abbrev[Chenpheno_abbrev$Region == "dorsomedialfrontal",1] <- "dorsomedial frontal"Chenpheno_abbrev[Chenpheno_abbrev$Region == "anteromedialtemporal",1] <- "anteromedial temporal"
###area####load("~/Desktop/2021lab/Hao/results_2Factor_UKB_raw/UKB_raw_area_CFA.Rdata")r <- area$results
index <- match(r$lhs, Chenpheno_abbrev$Shorttened_name, nomatch = 0)r$old_lhs <- r$lhs #for safety double check r$lhs[index != 0] <- Chenpheno_abbrev$Region[index]index <- match(r$rhs, Chenpheno_abbrev$Shorttened_name, nomatch = 0)r$old_rhs <- r$rhs #for safety double check r$rhs[index != 0] <- Chenpheno_abbrev$Region[index]
Ar_one
zeros <- data.frame (region = c("dorsolateral prefrontal", "dorsomedial frontal","motor-premotor"), STD_ALL = c(0,0,0))#F1 connectionsAr_one <- r[1:9,c(3,6)]colnames(Ar_one) <- c("region", "STD_ALL") Ar_one<- rbind(Ar_one,zeros)Ar_one%>% ggseg(atlas = "chenAr",mapping = aes(fill = STD_ALL))+ labs(title = "F1_area")+ scale_fill_gradientn(colours = c("lightgray","steelblue4"),na.value = "transparent")ggsave("F1_area.png", width = 10, height = 3)
#F2Ar_two <- r[12:19,c(3,6)]colnames(Ar_two) <- c("region", "STD_ALL") zeros <- data.frame (region = c("inferior parietal", "anteromedial temporal","superior parietal","posterolateral temporal"), STD_ALL = c(0,0,0,0))Ar_two<- rbind(Ar_two,zeros)Ar_two%>% ggseg(atlas = "chenAr",mapping = aes(fill = STD_ALL))+ labs(title = "F2_area")+ scale_fill_gradientn(colours = c("lightgray","steelblue4"),na.value = "transparent")ggsave("F2_area.png", width = 10, height = 3)
#####thickness######
load("~/Desktop/2021lab/Hao/results_2Factor_UKB_raw/UKB_raw_thickness_CFA.Rdata")r <- thickness$results
index <- match(r$lhs, Chenpheno_abbrev$Shorttened_name, nomatch = 0)r$old_lhs <- r$lhs #for safety double check r$lhs[index != 0] <- Chenpheno_abbrev$Region[index]index <- match(r$rhs, Chenpheno_abbrev$Shorttened_name, nomatch = 0)r$old_rhs <- r$rhs #for safety double check r$rhs[index != 0] <- Chenpheno_abbrev$Region[index]r$rhs
#F1 connections
Th_one <- r[1:10,c(3,6)]colnames(Th_one) <- c("region", "STD_ALL") zeros <- data.frame (region = c("temporal pole", "medial temporal"), STD_ALL = c(0,0))Th_one<- rbind(Th_one,zeros)
Th_one%>% ggseg(atlas = "chenTh",mapping = aes(fill = STD_ALL))+ labs(title = "F1_thickness")+ scale_fill_gradientn(colours = c("lightgray","steelblue4"),na.value = "transparent")ggsave("F1_thickness.png", width = 10, height = 3)

#F2Th_two <- r[13:21,c(3,6)]colnames(Th_two) <- c("region", "STD_ALL") zeros <- data.frame (region = c("motor-premotor-supplementary motor area", "inferior parietal", "occipital"), STD_ALL = c(0,0,0))Th_two<- rbind(Th_two,zeros)
Th_two%>% ggseg(atlas = "chenTh",mapping = aes(fill = STD_ALL))+ labs(title = "F2_thickness")+ scale_fill_gradientn(colours = c("lightgray","steelblue4"),na.value = "transparent")ggsave("F2_thickness.png", width = 10, height = 3)

2facor_brainmap_unified.R

unified scale

#2 factor brain map rm(list=ls())
setwd('/Users/nini/Desktop/2021lab/CH/brainmap/')library(ggsegChen)library(ggseg)library(dplyr)library(readxl)
Chenpheno_abbrev <- read.delim("/Users/nini/Desktop/2021lab/CH/brainmap/2factor_brainmap/Chenpheno_abbrev.txt") Chenpheno_abbrev$Region
Chenpheno_abbrev$Region<- gsub("_area", "", Chenpheno_abbrev$Region)Chenpheno_abbrev$Region<- gsub("_thickness", "", Chenpheno_abbrev$Region)Chenpheno_abbrev[Chenpheno_abbrev$Region == "ventromedialoccipital",1] <- "ventromedial occipital"Chenpheno_abbrev[Chenpheno_abbrev$Region == "ventralfrontal",1] <- "ventral frontal"Chenpheno_abbrev[Chenpheno_abbrev$Region == "temporalpole",1] <- "temporal pole"Chenpheno_abbrev[Chenpheno_abbrev$Region == "superiorparietal",1] <- "superior parietal"Chenpheno_abbrev[Chenpheno_abbrev$Region == "motor_premotor_SMA",1] <- "motor-premotor-supplementary motor area"Chenpheno_abbrev[Chenpheno_abbrev$Region == "middletemporal",1] <- "middle temporal"Chenpheno_abbrev[Chenpheno_abbrev$Region == "medialtemporal",1] <- "medial temporal"Chenpheno_abbrev[Chenpheno_abbrev$Region == "medialprefrontal",1] <- "medial prefrontal"Chenpheno_abbrev[Chenpheno_abbrev$Region == "inferiorparietal",1] <- "inferior parietal"Chenpheno_abbrev[Chenpheno_abbrev$Region == "dorsolateralprefrontal",1] <- "dorsolateral prefrontal"Chenpheno_abbrev[Chenpheno_abbrev$Region == "superiortemporal",1] <- "superior temporal"Chenpheno_abbrev[Chenpheno_abbrev$Region == "parsopercularis",1] <- "pars opercularis,subcentral"Chenpheno_abbrev[Chenpheno_abbrev$Region == "inferiorparietal",1] <- "inferior parietal"Chenpheno_abbrev[Chenpheno_abbrev$Region == "dorsolateralprefrontal",1] <- "dorsolateral prefrontal"Chenpheno_abbrev[Chenpheno_abbrev$Region == "superiorparietal",1] <- "superior parietal"Chenpheno_abbrev[Chenpheno_abbrev$Region == "posterolateraltemporal",1] <- "posterolateral temporal"Chenpheno_abbrev[Chenpheno_abbrev$Region == "motorpremotor",1] <- "motor-premotor"Chenpheno_abbrev[Chenpheno_abbrev$Region == "dorsomedialfrontal",1] <- "dorsomedial frontal"Chenpheno_abbrev[Chenpheno_abbrev$Region == "anteromedialtemporal",1] <- "anteromedial temporal"
###area####load("~/Desktop/2021lab/Hao/results_2Factor_UKB_raw/UKB_raw_area_CFA.Rdata")r <- area$results
index <- match(r$lhs, Chenpheno_abbrev$Shorttened_name, nomatch = 0)r$old_lhs <- r$lhs #for safety double check r$lhs[index != 0] <- Chenpheno_abbrev$Region[index]index <- match(r$rhs, Chenpheno_abbrev$Shorttened_name, nomatch = 0)r$old_rhs <- r$rhs #for safety double check r$rhs[index != 0] <- Chenpheno_abbrev$Region[index]
zeros <- data.frame (region = c("dorsolateral prefrontal", "dorsomedial frontal","motor-premotor"), STD_ALL = c(0,0,0))#F1 connectionsAr_one <- r[1:9,c(3,6)]colnames(Ar_one) <- c("region", "STD_ALL") Ar_one<- rbind(Ar_one,zeros)b <- c(0, 0.5,1)Ar_one%>% ggseg(atlas = "chenAr",mapping = aes(fill = STD_ALL))+ labs(title = "F1_area")+ scale_fill_gradientn(limits = c(-0.4,1.3), colours = c("lightgray","steelblue4"),na.value = "transparent", breaks=b,labels=format(b))ggsave("F1_area.png", width = 10, height = 3)

scale_col <- scale_fill_gradientn(limits = c(-0.4,1.3), colours = c("lightgray","steelblue4"),na.value = "transparent", breaks=b,labels=format(b))#F2Ar_two <- r[12:19,c(3,6)]colnames(Ar_two) <- c("region", "STD_ALL") zeros <- data.frame (region = c("inferior parietal", "anteromedial temporal","superior parietal","posterolateral temporal"), STD_ALL = c(0,0,0,0))Ar_two<- rbind(Ar_two,zeros)Ar_two%>% ggseg(atlas = "chenAr",mapping = aes(fill = STD_ALL))+ labs(title = "F2_area")+ scale_colggsave("F2_area.png", width = 10, height = 3)
#####thickness######
load("~/Desktop/2021lab/Hao/results_2Factor_UKB_raw/UKB_raw_thickness_CFA.Rdata")r <- thickness$results
index <- match(r$lhs, Chenpheno_abbrev$Shorttened_name, nomatch = 0)r$old_lhs <- r$lhs #for safety double check r$lhs[index != 0] <- Chenpheno_abbrev$Region[index]index <- match(r$rhs, Chenpheno_abbrev$Shorttened_name, nomatch = 0)r$old_rhs <- r$rhs #for safety double check r$rhs[index != 0] <- Chenpheno_abbrev$Region[index]r$rhs
#F1 connections
Th_one <- r[1:10,c(3,6)]colnames(Th_one) <- c("region", "STD_ALL") zeros <- data.frame (region = c("temporal pole", "medial temporal"), STD_ALL = c(0,0))Th_one<- rbind(Th_one,zeros)
Th_one%>% ggseg(atlas = "chenTh",mapping = aes(fill = STD_ALL))+ labs(title = "F1_thickness")+ scale_colggsave("F1_thickness.png", width = 10, height = 3)
#F2Th_two <- r[13:21,c(3,6)]colnames(Th_two) <- c("region", "STD_ALL") zeros <- data.frame (region = c("motor-premotor-supplementary motor area", "inferior parietal", "occipital"), STD_ALL = c(0,0,0))Th_two<- rbind(Th_two,zeros)
Th_two%>% ggseg(atlas = "chenTh",mapping = aes(fill = STD_ALL))+ labs(title = "F2_thickness")+ scale_colggsave("F2_thickness.png", width = 10, height = 3)

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