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

In antagomir/netresponse: Functional Network Analysis

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)

Author(s)

Leo Lahti [e-mail]

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) 

antagomir/netresponse documentation built on March 30, 2023, 7:24 a.m.