In epongpipat/ppi: Psychophysiological Interaction (PPI)

library(tidyverse)
library(kableExtra)

Data Wrangling

Hmisc::list.tree(params$data_wrangling, depth = 3)

Parameters

MRI

params_mri <- params$data_wrangling$params$mri %>%
  as.data.frame() %>%
  t() %>%
  as.data.frame() %>%
  rownames_to_column("parameter")
colnames(params_mri)[2] <- "value"
  kable(params_mri) %>%
  kable_styling(., bootstrap_options = c("striped", "hover", "condensed", "responsive"), full_width = F, position = "left")

PPI

params_ppi <- params$data_wrangling$params$ppi %>%
  as.data.frame() %>%
  t() %>%
  as.data.frame() %>%
  rownames_to_column("parameter")
colnames(params_ppi)[2] <- "value"
  kable(params_ppi) %>%
  kable_styling(., bootstrap_options = c("striped", "hover", "condensed", "responsive"), full_width = F, position = "left")

HRF

visualize_time_series(params$data_wrangling$params$hrf)

PSY Variables

Events

params$data_wrangling$psy_var$events %>% 
  kable() %>%
  kable_styling(., bootstrap_options = c("striped", "hover", "condensed", "responsive"), full_width = F, position = "left")

Trial Type by Volume

params$data_wrangling$psy_var$trial_type_by_volume %>%
  mutate(value = 0) %>%
  ggplot(., aes(volume, value, color = trial_type)) +
  geom_point() +
  theme_minimal() +
  labs(y = NULL) +
  theme(axis.text.y = element_blank(),
        axis.ticks.y = element_blank(),
        panel.grid.major.y = element_blank(),
        panel.grid.minor.y = element_blank(),
        legend.position="bottom")

Contrast Table

params$data_wrangling$psy_var$contrast_table %>%
  kable() %>%
  kable_styling(., bootstrap_options = c("striped", "hover", "condensed", "responsive"), full_width = F, position = "left")

Contrast

visualize_time_series(params$data_wrangling$psy_var$contrast, ncol = 1)

Upsample

params$data_wrangling$psy_var$upsample %>% visualize_time_series(., ncol = 1, scales = "free_y")

Convolve

params$data_wrangling$psy_var$convolve %>% visualize_time_series(., ncol = 1, scales = "free_y")

Downsample

params$data_wrangling$psy_var$downsample %>% visualize_time_series(., ncol = 1, scales = "free_y")

PHYS Variable

Input

params$data_wrangling$phys_var$input %>% visualize_time_series()

Detrend

params$data_wrangling$phys_var$detrend %>% visualize_time_series()

Upsample

params$data_wrangling$phys_var$upsample %>% visualize_time_series()

Deconvolve

params$data_wrangling$phys_var$deconvolve %>% visualize_time_series()

PPI Variable

Interaction

params$data_wrangling$ppi_var$interaction %>% visualize_time_series(., ncol = 1, scales = "free_y")

Convolve

params$data_wrangling$ppi_var$convolve %>% visualize_time_series(., ncol = 1, scales = "free_y")

Downsample

params$data_wrangling$ppi_var$downsample %>% visualize_time_series(., ncol = 1, scales = "free_y")

Design Matrix

params$data_wrangling$design_matrix %>% visualize_time_series_heatmap(., transpose = T, scale_data = "min-max", palette = "Greys", variable_axis_label = NULL, caption = "Note: Variables are scaled to min-max for visualization purposes")

Session Information

sessionInfo()

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