netresponse (version 1.32.2)

plot_matrix: Visualize a matrix with one or two-way color scale.

Description

Fast investigation of matrix objects; standard visualization choices are made automatically; fast and easy-to-use but does not necessarily provide optimal visualization.

Usage

plot_matrix(mat, type = "twoway", midpoint = 0, palette = NULL,
  colors = NULL, col.breaks = NULL, interval = 0.1, plot_axes = "both",
  row.tick = 1, col.tick = 1, cex.xlab = 0.9, cex.ylab = 0.9,
  xlab = NULL, ylab = NULL, limit.trunc = 0, mar = c(5, 4, 4, 2), ...)

Arguments

mat

matrix

type

String. Specifies visualization type. Options: 'oneway' (color scale ranges from white to dark red; the color can be changed if needed); 'twoway' (color scale ranges from dark blue through white to dark red; colors can be changed if needed)

midpoint

middle point for the color plot: smaller values are shown with blue, larger are shown with red in type = 'twoway'

palette

Optional. Color palette.

colors

Optional. Colors.

col.breaks

breakpoints for the color palette

interval

interval for palette color switches

plot_axes

String. Indicates whether to plot x-axis ('x'), y-axis ('y'), or both ('both').

row.tick

interval for plotting row axis texts

col.tick

interval for plotting column axis texts

cex.xlab

use this to specify distinct font size for the x axis

cex.ylab

use this to specify distinct font size for the y axis

xlab

optional x axis labels

ylab

optional y axis labels

limit.trunc

color scale limit breakpoint

mar

image margins

...

optional parameters to be passed to function 'image', see help(image) for further details

Value

• A list with the color palette (colors), color breakpoints (breaks), and palette function (palette.function)

References

See citation('microbiome')

Examples

mat <- rbind(c(1,2,3,4,5), c(1, 3, 1), c(4,2,2))
  plot_matrix(mat, 'twoway', midpoint = 3)