SomaDataIO (version 6.4.0)

plot.Map: 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 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,
  ...
)

Value

Plot an image of the passed matrix.

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.

Author

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)