ggheat.continuous.single: 'ggheat.continuous.single' ggheatmap function for plotting a...

In montilab/BS831: Boston University - Genomics Data Mining

ggheat.continuous.single ggheatmap function for plotting a single eset

Description

ggheat.continuous.single ggheatmap function for plotting a single eset

Usage

ggheat.continuous.single(
  eset,
  hc,
  hr,
  hmcolors = NA,
  hmtitle = "expression",
  col_lab,
  col_legend,
  ylabstr = "",
  fout = NA,
  p.heights = c(1.5, 0.5, 5),
  xsize = 4,
  ysize = 4,
  ysizelab = 7,
  xright = 0.24,
  override.hc = NA
)

Arguments

eset	expression set
hc	column clustering from hclust or hcopt
hr	row clustering from hclust or hcopt
hmcolors	function for heatmap color gradient, default: hmcolors<-function(... ) scale_fill_gradient2(low = "blue", mid = "white", high = "red", midpoint = 0, limits=c(-3,3), oob=squish, ...)
hmtitle	title of heatmap color label, default: "expression"
col_lab	column color label to display, one or more of columns of pData(eset)
col_legend	named list of column color legends, names correspond to col_lab, see format: col_legend<-list(COL1 = list(col_breaks = COL1levels, col_values = brewer.pal(length(COL1levels),"Set1"), col_labels = COL1levels), COL2 = list(col_breaks = COL2levels, col_values = brewer.pal(length(COL2levels),"Set2"), col_labels = COL2levels))
ylabstr	y axis title string,
fout	filename to save plot, default NA, save as object, to display to device, use grid.arrange
p.heights	panel heights default c(1.5, 0.5, 5),
xsize	default 4 x axis labels (uses colnames), set to 0 to turn off display
ysize	default 4, y axis labels (uses rownames), set to 0 to turn off display
ysizelab	default 7, text size for y axis title (specified in ylabstr)
xright	default 0.24, displayed width for right margin as fraction of whole plot width

Examples

#load expression data
data(tcga.subset.400g.200s)
dat

#hclust for rows and columns
hc<-clust_eset(dat)

pData(dat)$hclust.groups<-as.factor(cutree(hc$hc, k = 4))

#scale expression by row
dat.scaled<-scale_row(dat)

subtypelevels<-levels(dat$subtype)

#color legends for column labels
col_legend<-list(subtype = list(col_breaks = subtypelevels,
		col_values = brewer.pal(length(subtypelevels),"Set1"),
		col_labels = subtypelevels),
		hclust.groups = list(col_breaks = levels(pData(dat)$hclust.groups),
		col_values = sapply(c("pink", "orange", "yellow", "cyan"), to.hex),
		col_labels = levels(pData(dat)$hclust.groups)))

#heatmap fill gradient
hmcolors<-function(... ) scale_fill_gradient2(low = "blue", mid = "white",
       high = "red", midpoint = 0, limits=c(-3,3), oob=squish, ...)

p<-ggheat.continuous.single(eset = dat.scaled,
	hc = hc$hc,
	hr = hc$hr,
	hmcolors = hmcolors,
	hmtitle = "row-zscore GE",
	col_lab = c("subtype", "hclust.groups"),
	col_legend = col_legend,
	ylabstr = "",
	fout = NA,
	p.heights = c(1.5, 0.5, 5),
	xsize = 0,
	ysize = 0,
	ysizelab = 7,
	xright = 0.18

montilab/BS831 documentation built on April 17, 2024, 4:51 p.m.