In epongpipat/ppi: Psychophysiological Interaction (PPI)

R Packages

packages <- c("tidyverse", "eepR", "furrr", "ggpubr")
xfun::pkg_attach(packages, install = T, message = F)

script_dir <- "~/Documents/GitHub/ppi/R/"
script_files <- list.files(script_dir)
script_path <- paste0(script_dir, script_files)
script_ppi <- lapply(script_path, source)

Define Parameters

MRI

tr <- 1.5
n_volumes <- 260

Files

events_file <- "~/Box/my_mri/behavioral/nback_3tb4188_2017_Sep_13_1341_soa.csv"
out_file <- NULL

PPI Options

hrf_name <- "spmg1"
upsample_factor <- 16
detrend_factor <- 2

psy_contrast_table <- cbind(nback_vs_baseline = c(1, 1, 1, 1, -4)/5,
                                              task_vs_control = c(-3, 1, 1, 1, 0)/4,
                                              linear_task = c(0, -1, 0, 1, 0),
                                              quadratic_task = c(0, -1, 2, -1, 0)/3)
psy_contrast_table

Load Data

PSY

df_psy <- read.csv(events_file) %>%
  rename(onset = start, trial_type = block) %>%
  mutate(duration = ifelse(trial_type == "0-back", 10 * 2.5, 20 * 2.5)) %>%
  select(run, onset, duration, trial_type) %>%
  group_by(run) %>%
  nest() %>%
  mutate(data = map(data, as.data.frame)) %>%
  ungroup() %>%
  select(run, data_psy = data)

PHYS

dir_phys <- "/Volumes/shared/KK_KR_JLBS/Wave1/MRI/FMRI/PPI/Nback_individual_covariates/PHYS_MNI_42_-42_42/3tb1780/"
files_phys <- list.files(dir_phys, "_mean.1D")
path_phys <- paste0(dir_phys, files_phys)
df_phys <- tibble(file = files_phys,
                  path = path_phys) %>%
  mutate(run = str_remove(file, "_mean.1D"),
         run = str_remove(run, "r"),
         run = as.integer(run),
         data = future_map(path, function(x) read.csv(x, header = F, col.names = "data"))) %>%
  select(run, data_phys = data)

Data Wrangling

df_wrangling <- full_join(df_psy, df_phys, by = "run") %>%
  mutate(data_wrangling = NA)

for (i in 1:nrow(df_wrangling)) {
  df_wrangling$data_wrangling[i] <- list(data_wrangling(psy_events_data = df_wrangling$data_psy[[i]], 
                                          psy_contrast_table = psy_contrast_table, 
                                          phys_data = df_wrangling$data_phys[[i]],
                                          detrend_factor = 2, 
                                          hrf_name = "spmg1",
                                          tr = 1.5, 
                                          n_volumes = 260, 
                                          upsample_factor = 16, 
                                          deconvolve = TRUE))
}

Design Matrix

df_design_mat <- df_wrangling %>%
  mutate(design_mat = map(data_wrangling, "design_matrix")) %>%
  select(run, design_mat) %>%
  unnest()

head(df_design_mat)

func_fig_data_heat_map <- function(data) {
  colnames(data) <- paste0(str_pad(1:ncol(data), 2, "left", "0"), "_", colnames(data))
  apply(data, 2, scale_min_max) %>%
    as.data.frame() %>%
    mutate(volume = row_number()) %>%
    gather(., variable, value, -volume) %>%
    ggplot(., aes(variable, volume, fill = value)) +
    geom_raster() + 
    scale_fill_distiller(palette = "Greys", direction = 1) + 
    theme_minimal() +
    theme(axis.text.x = element_text(hjust = 1, angle = 45)) +
    labs(x = NULL)
}

func_fig_data_ts_long <- function(data) {
  colnames(data) <- paste0(str_pad(1:ncol(data), 2, "left", "0"), "_", colnames(data))
  data %>%
  mutate(volume = row_number()) %>%
  gather(., variable, value, -volume) %>%
  ggplot(., aes(volume, value)) +
  geom_line() +
  facet_wrap(~ variable, scales = "free_y", ncol = 1) +
  theme_minimal()
}

func_fig_data_heat_map(df_design_mat)

func_fig_data_ts_long(df_design_mat)

Save

if (!is.null(out_file)) {
  write.csv(df_design_mat_final, out_file)
}

epongpipat/ppi documentation built on Jan. 31, 2024, 1:02 p.m.