heatmapPlotWrapper: Wrapper function, plotting the heatmap

Description

This function is package internal and should not be executed directly by users.

Usage

heatmapPlotWrapper(MAT, axhline = NULL, titles = rep("", length(MAT)),
  bins = 1:(ncol(MAT[[1]])/length(MAT)), cex.lab = 12, cex.axis = 12,
  cex.legend = 12, xlab = "", ylab = "", Leg = TRUE, autoscale = TRUE,
  zmin = 0, zmax = 10, xlim = NULL, ln.v = TRUE, e = NULL, s = 0.01,
  indi = TRUE, o_min = NA, o_max = NA, colvec = NULL,
  colorspace = NULL, pointsize = 12, embed = FALSE, raster = FALSE,
  ylim = c(nrow(MAT[[1]]), 1), dendro = NULL, ...)

Arguments

MAT

- list of matrixes holding heatmap data

axhline

- locations of horizontal lines separating the clusters

titles

the sub-titles of heatmaps

bins

the x-axis indicates in heatmap

cex.lab

Axis labels font size in points, Defaults to 12

cex.axis

Axis numbers font size in points, defaults to 12

cex.legend

Keys labels font size in points, defaults to 12

xlab

label below x-axis

ylab

label below y-axis

autoscale

if TRUE the color keys will be auto scaled

zmin

global minimum value on color key, ignored if autoscale is TRUE

zmax

global maximum value on color key, ignored if autoscale is TRUE

xlim

the x limits (x1, x2) of the plot. Note that x1 > x2 is allowed and leads to a "reversed axis". The default value, NULL, indicates that the whole range present in plotset will be plotted.

ln.v

Determines if vertical guide line(s) should be plotted (TRUE) or ommitted (FALSE). For anchored plots 2 lines indicating the start and end of anchored distance are plotted.

Determines the end of anchored distance

The saturation value used to auto scale color key limits, defaults to 0.01

indi

If TRUE (defaults) the independent color keys will be plotted below heatmaps, if FALSE the common color key is shown rightmost

o_min

vector of length equal to number of sub heatmaps determining minimum value on color key for each sub plot, if NULL (default) or NA the global settings are used, ignored in indi is FALSE

o_max

vector of length equal to number of sub heatmaps determining maximum value on color key for each sub plot, if NULL (default) or NA the global settings are used, ignored in indi is FALSE

colvec

The vector of colors used to plot the lines and error estimate fields. If set value NULL (default) the automatically generated color values will be used. Accepted values are: vector of any of the three kinds of R color specifications, i.e., either a color name (as listed by colors()), a hexadecimal string of the form "#rrggbb" or "#rrggbbaa" (see rgb), or a positive integer i meaning palette()[i]. See col2rgb.

colorspace

The colorspace of the heatmap, see grDevices

pointsize

The default font point size to be used for plots. Defaults to 12 (1/72 inch).

embed

Configures heatmap to be used embedded plot. Defaults to FALSE

raster

Uses raster graphics for heatmaps. Defaults to FALSE

ylim

Y axis limits. Defaults to c(nrow(MAT[[1]]),1)

dendro

Dendrogram object, will be plotted left to heatmaps. Defaults to NULL

leg

if TRUE plot the color key

Value

NULL