Plotting brain images with ggseg

ggseg plotting brain images with R

• ggesg package details for creating brain figures right in R
• More info available in the publication: Visualization of Brain Statistics With R Packages ggseg and ggseg3d
• Our reproducible example script for plotting structural images in R

Output

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Notes

• works on the output of running all models on dk atlas, example found in this private repository
• the code below helps clean the significant model output into a data frame compatible with ggseg
• cleans strings for ggseg
• prepare hemisphere column

ggseg_df <- sig_models %>%
  select(brain_var, estimate, statistic, p.value) %>%
  # scale estimate for plotting
  mutate(beta = scale(estimate)) %>%
  # remove freesurfer prefix
  mutate_at("brain_var", str_remove, "fs_") %>%
  # remove gray vol suffix
  mutate_at("brain_var", str_remove, "_grayvol") %>%
  # create hemisphere variable based on string
  mutate(hemi = case_when(
    grepl("^l_", brain_var) ~ "left",
    grepl("^r_", brain_var) ~ "right",
    TRUE ~ "both/other"
  )) %>%
  # clean up l and r string
  mutate(brain_var = str_remove(brain_var, "l_")) %>%
  mutate(brain_var = str_remove(brain_var, "r_"))

• manual rename of brain vars in order to work with ggseg
• there might be built-in solutions for this in package vignettes

ggseg_dat <- ggseg_df %>%
  mutate(region = case_when(
    brain_var == "bankssts" ~ "bankssts",
    brain_var == "caudalanteriorcingulate" ~ "caudal anterior cingulate",
    brain_var == "caudalmiddlefrontal" ~ "caudal middle frontal",
    # brain_var == "corpus callosum",
    brain_var == "cuneus" ~ "cuneus",
    brain_var == "entorhinal" ~ "entorhinal",
    brain_var == "frontalpole" ~ "frontal pole",
    brain_var == "fusiform" ~ "fusiform",
    brain_var == "inferiorparietal" ~ "inferior parietal",
    brain_var == "inferiortemporal" ~ "inferior temporal",
    brain_var == "insula" ~ "insula",
    brain_var == "isthmuscingulate" ~ "isthmus cingulate",
    brain_var == "lateraloccipital" ~ "lateral occipital",
    brain_var == "lateralorbitofrontal" ~ "lateral orbitofrontal",
    brain_var == "lingual" ~ "lingual",
    brain_var == "medialorbitofrontal" ~ "medial orbitofrontal",
    brain_var == "middletemporal" ~ "middle temporal",
    brain_var == "paracentral" ~ "paracentral",
    brain_var == "parahippocampal" ~ "parahippocampal",
    brain_var == "parsopercularis" ~ "pars opercularis",
    brain_var == "parsorbitalis" ~ "pars orbitalis",
    brain_var == "parstriangularis" ~ "pars triangularis",
    brain_var == "pericalcarine" ~ "pericalcarine",
    brain_var == "postcentral" ~ "postcentral",
    brain_var == "posteriorcingulate" ~ "posterior cingulate",
    brain_var == "precentral" ~ "precentral",
    brain_var == "precuneus" ~ "precuneus",
    brain_var == "rostralanteriorcingulate" ~ "rostral anterior cingulate",
    brain_var == "rostralmiddlefrontal" ~ "rostral middle frontal",
    brain_var == "superiorfrontal" ~ "superior frontal",
    brain_var == "superiorparietal" ~ "superior parietal",
    brain_var == "superiortemporal" ~ "superior temporal",
    brain_var == "supramarginal" ~ "supramarginal",
    brain_var == "temporalpole" ~ "temporal pole",
    brain_var == "transversetemporal" ~ "transverse temporal"
  ))