drawHeatMap: Draw a heat map for a given variable

In wanyuac/GeneMates: Analysing association and physical linkage between bacterial genes

Draw a heat map for a given variable

Description

This is a generic function for plotting a heat map given two ID variables and a value variable.

Usage

drawHeatMap(
  data = NULL,
  x = "x",
  y = "y",
  val = "val",
  diag = 1,
  replace.na = 0,
  cluster.row = TRUE,
  cluster.col = TRUE,
  cluster.method = "complete",
  dist.row = "euclidean",
  dist.col = "euclidean",
  colour.low = "white",
  colour.mid = NULL,
  colour.high = "red",
  colour.grad = 50,
  colour.breaks,
  display.val = FALSE,
  font.size = 10,
  filename = "heatmap.png",
  res = 72,
  width = 800,
  height = 800,
  unit = "px"
)

Arguments

data	A data frame of at least three columns, such as x, y and z, or a matrix to be plotted directly as a heat map.
x	Name (character) of the first variable of IDs.
y	Name (character) of the second variable of IDs.
val	Name (character) or index (integer) of the variable for values in the heat matrix.
diag	The value of diagonal cells in the unclustered heat map.
replace.na	The value used to replace NA's.
cluster.row	Whether cluster rows hierarchically.
cluster.col	Whether cluster columns hierarchically.
cluster.method	The method for hierarchical clustering.
dist.row	The distance metric for hierarchical clustering of rows.
dist.col	The distance metric for hierarchical clustering of columns.
colour.low	The colour for the lowest value in the heat matrix.
colour.mid	The colour for the middle (that is, the "zero") value. Set to NULL if only a single colour transition are to be included.
colour.high	The colour for the highest value.
colour.grad	The number of colour grades.
colour.breaks	Break points (colour.grad + 1) of values for assigning colours.
display.val	A boolean value determining whether to overlay values on the heat map or not.
font.size	Font size of labels in the heat map.
filename	Path and name for the output PNG image.
res	Resolution of the output figure. Default: 72 ppi.
width	Width of the output image.
height	Height of the output image.
unit	The unit of the width and height of the output image. Valid values: "mm" and "px" (default).

Author(s)

Yu Wan ([e-mail])

wanyuac/GeneMates documentation built on Aug. 12, 2022, 7:37 a.m.