library(dplyr)
library(stringr)
library(readxl)
library(tidyr)
library(arsenal)
library(ggplot2)
library(caret)
library(tidyverse)
library(randomForest)
library(nnet)
library(e1071)
library(rpart)
library(tree)
library(glmnet)
library(writexl)
library(broom)
library(class)
library(xgboost)
library(ggplot2)
library(ggpubr)
library(readxl)
library(ggseg)
library(ggplot2)
library(neuroCombat)
library(viridis)
library(scales)
library(ggsegGlasser)
load("C:/Users/Bronny/Desktop/bio/summer/anxietysubtype.RData")
df <- data.frame(SCFC_anx)
df <- as.data.frame(t(df))
df$subjectkey <- rownames(df)
df$subjectkey <- sub("^(NDAR)", "\\1_", df$subjectkey)
df1 <- merge(anx_sub_bl_filtered,df,by="subjectkey")
df1[is.na(df1)] <- 0
df4 <- df1 %>% select(-c(1:10))
colnames(df4)[2:380] <- mmp_subcor
df4.1 <- df4[,-1]
df4_transformed <- as.data.frame(lapply(df4.1, function(r) sqrt(376)*0.5 * log((1 + r) / (1 - r))))
df4_transformed <- cbind(df4[, 1], df4_transformed)
colnames(df4_transformed)[1] <- colnames(df4)[1]
df4_transformed$subtype <- as.factor(df4_transformed$subtype)
p_values <- numeric(379)
tukey_p_values <- list()
for (i in 1:379) {
model <- aov(df4_transformed[[i + 1]] ~ subtype, data = df4_transformed)
p_value <- summary(model)[[1]][["Pr(>F)"]][1]
p_values[i] <- p_value
if (p_value < 0.05) {
tukey_result <- TukeyHSD(model)
tukey_p_values[[colnames(df4_transformed)[i + 1]]] <- tukey_result$subtype[, "p adj"]
}
}
fdr_adjusted_p_values <- p.adjust(p_values, method = "fdr")
names(p_values) <- colnames(df4_transformed)[2:380]
significant_columns <- p_values[p_values < 0.05]
tukey_p_values
## $L_V6_ROI
## Separation-GAD Social-GAD
## 0.44427019 0.08200556
## Specific Phobia-GAD Social-Separation
## 0.02735210 0.99968296
## Specific Phobia-Separation Specific Phobia-Social
## 0.99930544 0.97606757
##
## $L_V3A_ROI
## Separation-GAD Social-GAD
## 0.59344394 0.03223409
## Specific Phobia-GAD Social-Separation
## 0.61343899 0.94138040
## Specific Phobia-Separation Specific Phobia-Social
## 0.88787064 0.07375565
##
## $L_LO2_ROI
## Separation-GAD Social-GAD
## 0.98087241 0.09148504
## Specific Phobia-GAD Social-Separation
## 0.99131864 0.64858416
## Specific Phobia-Separation Specific Phobia-Social
## 0.99343838 0.02714095
##
## $L_d23ab_ROI
## Separation-GAD Social-GAD
## 0.64549748 0.02815465
## Specific Phobia-GAD Social-Separation
## 0.18037599 0.90406155
## Specific Phobia-Separation Specific Phobia-Social
## 0.99745062 0.32279819
##
## $L_7PL_ROI
## Separation-GAD Social-GAD
## 0.04458231 0.16849472
## Specific Phobia-GAD Social-Separation
## 0.28238077 0.60099293
## Specific Phobia-Separation Specific Phobia-Social
## 0.21499462 0.76307855
##
## $L_1_ROI
## Separation-GAD Social-GAD
## 0.01356771 0.33645173
## Specific Phobia-GAD Social-Separation
## 0.68581460 0.22879877
## Specific Phobia-Separation Specific Phobia-Social
## 0.03023858 0.66756181
##
## $L_2_ROI
## Separation-GAD Social-GAD
## 0.1883137 0.5428202
## Specific Phobia-GAD Social-Separation
## 0.9998228 0.6848893
## Specific Phobia-Separation Specific Phobia-Social
## 0.1069117 0.2570919
##
## $L_6v_ROI
## Separation-GAD Social-GAD
## 0.54887329 0.06589222
## Specific Phobia-GAD Social-Separation
## 0.94519160 0.98854178
## Specific Phobia-Separation Specific Phobia-Social
## 0.64893573 0.03392365
##
## $L_8BM_ROI
## Separation-GAD Social-GAD
## 0.25786357 0.03890590
## Specific Phobia-GAD Social-Separation
## 0.83682055 0.99993916
## Specific Phobia-Separation Specific Phobia-Social
## 0.39059586 0.03489228
##
## $L_8C_ROI
## Separation-GAD Social-GAD
## 0.67814547 0.32795806
## Specific Phobia-GAD Social-Separation
## 0.96090243 0.11523103
## Specific Phobia-Separation Specific Phobia-Social
## 0.76462000 0.03411871
##
## $L_a47r_ROI
## Separation-GAD Social-GAD
## 0.98570768 0.85799288
## Specific Phobia-GAD Social-Separation
## 0.49884050 0.99790969
## Specific Phobia-Separation Specific Phobia-Social
## 0.65738599 0.07530761
##
## $L_TE1p_ROI
## Separation-GAD Social-GAD
## 0.97492750 0.16811669
## Specific Phobia-GAD Social-Separation
## 0.99970960 0.78019438
## Specific Phobia-Separation Specific Phobia-Social
## 0.95466439 0.02623365
##
## $L_V3CD_ROI
## Separation-GAD Social-GAD
## 0.01006131 0.04687358
## Specific Phobia-GAD Social-Separation
## 0.32047255 0.51047358
## Specific Phobia-Separation Specific Phobia-Social
## 0.05550972 0.29001574
##
## $L_MBelt_ROI
## Separation-GAD Social-GAD
## 0.11952860 0.08181251
## Specific Phobia-GAD Social-Separation
## 0.27776997 0.92330940
## Specific Phobia-Separation Specific Phobia-Social
## 0.44870807 0.50318716
##
## $L_TE1m_ROI
## Separation-GAD Social-GAD
## 0.570306224 0.065354849
## Specific Phobia-GAD Social-Separation
## 0.005875619 0.984443034
## Specific Phobia-Separation Specific Phobia-Social
## 0.982998970 0.999940421
##
## $R_V3_ROI
## Separation-GAD Social-GAD
## 0.90811562 0.27611832
## Specific Phobia-GAD Social-Separation
## 0.94355625 0.95344444
## Specific Phobia-Separation Specific Phobia-Social
## 0.71875165 0.01896348
##
## $R_V3A_ROI
## Separation-GAD Social-GAD
## 0.06327389 0.09451498
## Specific Phobia-GAD Social-Separation
## 0.47386738 0.78716645
## Specific Phobia-Separation Specific Phobia-Social
## 0.19996652 0.34729848
##
## $R_V3B_ROI
## Separation-GAD Social-GAD
## 0.44744925 0.99911365
## Specific Phobia-GAD Social-Separation
## 0.52155457 0.50848645
## Specific Phobia-Separation Specific Phobia-Social
## 0.07879906 0.43066517
##
## $R_7PC_ROI
## Separation-GAD Social-GAD
## 0.15786970 0.65724198
## Specific Phobia-GAD Social-Separation
## 0.99932795 0.55481386
## Specific Phobia-Separation Specific Phobia-Social
## 0.08045678 0.35552744
##
## $R_MIP_ROI
## Separation-GAD Social-GAD
## 0.009416122 0.796679906
## Specific Phobia-GAD Social-Separation
## 0.974673030 0.057843013
## Specific Phobia-Separation Specific Phobia-Social
## 0.006394011 0.855902330
##
## $R_p9.46v_ROI
## Separation-GAD Social-GAD
## 0.45456605 0.01229641
## Specific Phobia-GAD Social-Separation
## 0.34115103 0.94261875
## Specific Phobia-Separation Specific Phobia-Social
## 0.88801127 0.07546763
##
## $R_9a_ROI
## Separation-GAD Social-GAD
## 0.02438999 0.18087316
## Specific Phobia-GAD Social-Separation
## 0.26855477 0.45101823
## Specific Phobia-Separation Specific Phobia-Social
## 0.13640962 0.80390247
##
## $R_AIP_ROI
## Separation-GAD Social-GAD
## 0.10842106 0.77931803
## Specific Phobia-GAD Social-Separation
## 0.99491666 0.36787922
## Specific Phobia-Separation Specific Phobia-Social
## 0.04159806 0.44469726
##
## $R_EC_ROI
## Separation-GAD Social-GAD
## 0.90017384 0.10564892
## Specific Phobia-GAD Social-Separation
## 0.02830712 0.84602324
## Specific Phobia-Separation Specific Phobia-Social
## 0.87451746 0.99204874
##
## $R_STSda_ROI
## Separation-GAD Social-GAD
## 0.73973024 0.03292150
## Specific Phobia-GAD Social-Separation
## 0.03956518 0.85519184
## Specific Phobia-Separation Specific Phobia-Social
## 0.98774954 0.74638137
##
## $R_VMV1_ROI
## Separation-GAD Social-GAD
## 0.004799139 0.869318530
## Specific Phobia-GAD Social-Separation
## 0.170250229 0.025536119
## Specific Phobia-Separation Specific Phobia-Social
## 0.047584714 0.754604775
for (roi in names(tukey_p_values)) {
tukey_res <- tukey_p_values[[roi]]
significant_comparisons <- names(tukey_res[tukey_res < 0.05])
my_comparisons <- lapply(significant_comparisons, function(comp) {
unlist(strsplit(comp, "-"))
})
df5 <- df4_transformed %>% select(subtype, roi)
colnames(df5)[2] <- "value"
p <- ggboxplot(df5, x = "subtype", y = "value",
color = "subtype", palette = "jco") +
stat_compare_means(comparisons = my_comparisons,
label = "p.format",
method = "t.test") +
theme_minimal() +
ggtitle(paste(roi))
print(p)
}
