plot.Map: Plot Image Maps

In SomaDataIO: Input/Output 'SomaScan' Data

Plot Image Maps

Description

Plotting function for objects of the outlier_map class. Produces a heatmap-style image using ggplot2 syntax, for objects produced by calcOutlierMap().

Usage

## S3 method for class 'Map'
plot(
  x,
  color.scheme = NULL,
  legend.ticks = 7,
  gridlines = NULL,
  gridlinecol = "red",
  gridlinelwd = 0.5,
  gridlinelty = 2,
  main = NULL,
  y.lab = NULL,
  x.lab = NULL,
  flags = NULL,
  legend.width = 1,
  legend.height = 2,
  filename = NULL,
  plot.width = 14,
  plot.height = 8,
  plot.scale = 1,
  ...
)

Arguments

x	An object of class: outlier_map
color.scheme	Which color scheme to use. Typical choices include: gplots::redgreen() gplots::bluered() grDevices::heat.colors() grDevices::terrain.colors() grDevices::topo.colors() RColorBrewer::brewer.pal() viridis::viridis() viridis::magma()
legend.ticks	How many ticks to place on the color legend.
gridlines	Numeric vector or logical. Indicates where to draw the horizontal grid lines that can be used to separate samples (rows). This should be a vector of the cumulative sum of the horizontal lines to be drawn, typically something like cumsum(table(data$Sex)). Alternatively, TRUE can be passed whereby the lines are determined by the "class.tab" element of x$class.tab (if possible).
gridlinecol	Color of the gridlines.
gridlinelwd	Width of the gridlines.
gridlinelty	Line type of the gridlines.
main	Character. Main title for the plot. See ggplot2::ggtitle() for ggplot2 style graphics.
y.lab	Character. Optional string for the y-axis. Otherwise one is automatically generated (default).
x.lab	Character. Optional string for the x-axis. Otherwise one is automatically generated (default).
flags	Numeric in ⁠[0, 1]⁠. For an "outlier_map", the proportion of the analytes (columns) for a given sample that must be outliers for a flag to be placed at the right-axis, right-axis, thus flagging that sample. If NULL (default), 0.05 (5%) is selected.
legend.width	Width for the color legend.
legend.height	Height for the color legend.
filename	Optional. If provided, the plot will be written to a file. The file name must also include the desired file type extension; this will be used to determine the file type, e.g. a file named foo.png will be saved as a PNG. See ggplot2::ggsave() for a full list of file type (device) options.
plot.width	If "filename != NULL", the width of the plot image file.
plot.height	If "filename != NULL", the height of the plot image file.
plot.scale	If "filename != NULL", the scale of the plot image file.
...	Arguments required by the plot() generic. Currently unused.

Value

Plot an image of the passed matrix.

Author(s)

Stu Field, Amanda Hiser

See Also

ggplot2::ggplot(), ggplot2::geom_raster()

Other Calc Map: calcOutlierMap(), getOutlierIds()

Examples

example_data |>
  dplyr::filter(SampleType == "Sample") |>
  head(10) |>
  calcOutlierMap() |>
  plot(flags = 0.05)

SomaDataIO documentation built on June 8, 2025, 10:13 a.m.