inst/doc/ggseg.R

In ggseg: Plotting Tool for Brain Atlases

## ----include = FALSE----------------------------------------------------------
knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>",
  fig.width = 6
)

## ----setup--------------------------------------------------------------------
library(ggseg)
library(ggplot2)

## -----------------------------------------------------------------------------
library(ggseg)
dk$atlas
dk$type
dk$palette
dk$data

## -----------------------------------------------------------------------------
plot(dk$data)

## -----------------------------------------------------------------------------
plot(dk)

## -----------------------------------------------------------------------------
dk

## -----------------------------------------------------------------------------
brain_regions(dk)
brain_labels(dk)

## -----------------------------------------------------------------------------
ggplot() +
  geom_brain(atlas = dk)

## -----------------------------------------------------------------------------
ggplot() +
  geom_brain(atlas = dk, position = position_brain(hemi ~ side))

## -----------------------------------------------------------------------------
cortical_pos <- c(
  "left lateral",
  "left medial",
  "right medial",
  "right lateral"
)
ggplot() +
  geom_brain(atlas = dk, position = position_brain(cortical_pos))

# Which can easily be switched around!
cortical_pos <- c(
  "right lateral",
  "left medial",
  "right medial",
  "left lateral"
)

ggplot() +
  geom_brain(atlas = dk, position = position_brain(cortical_pos))

## -----------------------------------------------------------------------------
ggplot() +
  geom_brain(atlas = dk, side = "lateral")

ggplot() +
  geom_brain(atlas = dk, hemi = "left")

## -----------------------------------------------------------------------------
ggplot() +
  geom_brain(atlas = aseg, side = "coronal", hemi = "left")

## -----------------------------------------------------------------------------
library(dplyr)

some_data <- tibble(
  region = c(
    "transverse temporal",
    "insula",
    "precentral",
    "superior parietal"
  ),
  p = sample(seq(0, .5, .001), 4)
)

some_data

## -----------------------------------------------------------------------------
ggplot(some_data) +
  geom_brain(
    atlas = dk,
    position = position_brain(hemi ~ side),
    aes(fill = p)
  ) +
  scale_fill_viridis_c(option = "cividis", direction = -1) +
  theme_void() +
  labs(
    title = "My awesome title",
    subtitle = "of a brain atlas plot",
    caption = "I'm pretty happy about this!"
  )

## -----------------------------------------------------------------------------
some_data <- tibble(
  region = rep(
    c(
      "transverse temporal",
      "insula",
      "precentral",
      "superior parietal"
    ),
    2
  ),
  p = sample(seq(0, .5, .001), 8),
  groups = c(rep("g1", 4), rep("g2", 4))
)

some_data

## -----------------------------------------------------------------------------
some_data |>
  group_by(groups) |>
  ggplot() +
  geom_brain(
    atlas = dk,
    position = position_brain(hemi ~ side),
    aes(fill = p)
  ) +
  facet_wrap(~groups) +
  ggtitle("correct facetting")

## -----------------------------------------------------------------------------
plot(dk)

## -----------------------------------------------------------------------------

data <- data.frame(
  region = brain_regions(dk)[1:3],
  reg_col = brain_regions(dk)[1:3]
)

data

ggplot(data) +
  geom_brain(atlas = dk, aes(fill = reg_col)) +
  scale_fill_brain2(dk$palette[data$region])

## -----------------------------------------------------------------------------
ggseg(
  some_data,
  atlas = dk,
  colour = "black",
  size = .1,
  position = "stacked",
  mapping = aes(fill = p)
)