functional_connectivity.Rmd

---
title: "functional_connectivity"
author: "Julia Gallucci"
date: "26/01/2023"
output: html_document
---

```{r setup, include=FALSE}
knitr::opts_chunk$set(echo = TRUE)
```

```{r}
#load libraries
library(corrr)
library(readr)
library(psych)
```

```{r}
# create file list of resting-state time series 
files_rest_ts <- list.files(path= ".", recursive=T, full.names=F, pattern="^.*_RS_6mm_GSR_glasser_tian_meants.csv$")

# create list of IDs
ptlist <- scan("/projects/jgallucci/SPINS_PNSC_DTI_RTMSWM/all_sub.txt", what="", sep="\n")

# read in time series files
rest_ts <- lapply(files_rest_ts, read_csv, col_names = FALSE)

# transpose time series
rest_ts <- lapply(rest_ts, t)

# Name each rs dataframe with subids
names(rest_ts) <- ptlist

# Read in glassier and tien atlas info
G_atlas_info <- read.csv(file = "/projects/loliver/SPINS_PLS_Conn/data/parcellations/Glasser_Tian_roi_info.csv", header=T)

# add labels to df columns
for (i in names(rest_ts)) {
  colnames(rest_ts[[i]]) <- as.vector(G_atlas_info$atlas_roi)
  rest_ts[[i]] <- data.frame(rest_ts[[i]])
}

#generate cor matrices for each participant
rest_cor <- lapply(rest_ts, correlate)

#extract lower triangle
rest_cor <- lapply(rest_cor, shave)

# create individual dataframes with cor matrices for each participant
rest_cor_str <- lapply(rest_cor, stretch, na.rm=F)
rest_cor_stru <- lapply(rest_cor_str, unite, col="rois", 1:2, sep="-", remove=T)
rest_cor_df <- lapply(rest_cor_stru, data.frame)
cor_names <- as.vector(rest_cor_df[[1]][,1])
for (i in names(rest_cor_df)) {
  rest_cor_df[[i]] <- data.frame(rest_cor_df[[i]][,2])
  rest_cor_df[[i]] <- t(rest_cor_df[[i]])
  colnames(rest_cor_df[[i]]) <- cor_names
}

# bind rows across df list to generate tibble with all corrs for each participant
rest_corrs <- do.call("rbind",rest_cor_df)
rownames(rest_corrs) <- names(rest_cor_df)

# remove columns with only NAs
rest_corrs <- rest_corrs[,colSums(is.na(rest_corrs)) != nrow(rest_corrs)]

# fisher z transform corrs
rest_corrs_z  <- fisherz(rest_corrs)
```