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Plot tract profiles

Source: R/plot.R
plot_tract_profiles.Rd

Create tract profile figures for each tract as a facet and for each y value as a figure.

Usage

plot_tract_profiles(
  df,
  y,
  tracts = NULL,
  tract_col = "tractID",
  node_col = "nodeID",
  group_col = NULL,
  n_groups = NULL,
  group_pal = "cb",
  participant_col = "subjectID",
  ribbon_func = "mean_cl_boot",
  ribbon_alpha = 0.25,
  linewidth = 1,
  save_figure = TRUE,
  output_dir = getwd(),
  ...
)

Arguments

df

The input dataframe.

y

Column name(s) of the variables to plot on the y-axis.

tracts

Name(s) of the tract tracts to plot per facet. Default: NULL

If NULL, will be all tracts in the data frame.

tract_col

The column name that encodes the tract information. Default: tractID

node_col

The column name that encodes tract node positions. Default: "nodeID".

group_col

Column name that encodes group information. Will be drawn by color. Default: NULL.

  • If group_col is a factor, will use unique values as groups.

  • If group_col is a numeric, will use ggplot2::cut_interval to create equal range n_groups as groups.

n_groups

Number of groups to split a numeric grouping variable. Only used if group_col is numeric. Default: NULL.

group_pal

Grouping color palette name. Valid options include: "cb" (colorblind), "cbb" (colorblind_black), and all named RColorBrewer palettes. Default: "cb" (colorblind)

participant_col

The column name that encodes participant ID. Default: "subjectID".

ribbon_func

Ribbon summarizing function that provides the y, ymin, and ymax for the ribbon. See fun.data argument from ggplot2::stat_summary for more information. Default: "mean_cl_boot"

ribbon_alpha

Ribbon alpha level. Default: 0.25

linewidth

Line thickness of the tract profile line. Default: 1.

save_figure

Boolean flag. If TRUE, save tract profiles. If FALSE, do not save tract profiles. Default: FALSE

output_dir

Output directory for the figure image(s). Default: getwd (current working directory).

...

Keyword arguments to be passed to ggplot2::ggsave.

Value

Named list of plot handles corresponding to the specified y values.

Details

If save_figure is TRUE, the naming convention is as follows:

  • If group_col, "tract_by-(group_col)_param-(y)_profiles.png".

  • If group_col == NULL, "tract_param-(y)_profiles.png"

Examples

if (FALSE) { # \dontrun{
df_sarica <- read_afq_sarica(na_omit = TRUE)

plot_handle <- plot_tract_profiles(
  df        = df,
  y         = c("fa", "md"),
  tracts    = c("Left Corticospinal", "Right Corticospinal"),
  width     = 12, 
  height    = 6,
  units     = "in"
)

plot_handle <- plot_tract_profiles(
  df        = df,
  y         = c("fa", "md"),
  tracts    = c("Left Corticospinal", "Right Corticospinal"),
  group_col = "group", 
  width     = 12, 
  height    = 6,
  units     = "in"
)

plot_handle <- plot_tract_profiles(
  df        = df,
  y         = "fa",
  tracts    = c("Left Corticospinal", "Right Corticospinal"),
  group_col = "age", 
  n_groups  = 5, 
  group_pal = "Spectral", 
  width     = 12, 
  height    = 6,
  units     = "in"
)} # }