heatmapPlotWrapper: Wrapper function, plotting the heatmap

In Przemol/seqplots-release: An interactive tool for visualizing NGS signals and sequence motif densities along genomic features using average plots and heatmaps.

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.
e	Determines the end of anchored distance
s	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

Przemol/seqplots-release documentation built on May 8, 2019, 3:47 a.m.