plot.dcmatrix {dcortools}

Plots a heatmap from a dcmatrix object using the function "pheatmap" from the package "pheatmap".

Description

Plots a heatmap from a dcmatrix object using the function "pheatmap" from the package "pheatmap".

Usage

## S3 method for class 'dcmatrix'
plot(
  x,
  type = "dcor",
  trunc.up = NULL,
  trunc.low = NULL,
  cluster_rows = FALSE,
  cluster_cols = FALSE,
  display_numbers = TRUE,
  ...
)

Arguments

x

a dcmatrix object.

type

specifies what should be displayed in the heatmap. One of "dcor", "dcov", "logp" (-log10 of corresponding p-values), "cor", "abscor" (absolute correlation), "logp.cor", "dcor.pw", "dcov.pw" or "logp.pw".

trunc.up

truncates the values to be plotted; if set to numeric, all values larger than trunc.up are set to trunc.up.

trunc.low

truncates the values to be plotted; if set to numeric, all values smaller than trunc.low are set to trunc.low.

cluster_rows, cluster_cols, display_numbers

passed to pheatmap().

...

passed to pheatmap().

Value

a heatmap plotting the entries of the slot specified in type of the object specified in dcmat.