plot heatmap

Plot a heatmap for counts.

plotHeatmap(
  se,
  facet = as.formula("group~sample"),
  transformFUN = log2,
  pseudo = 1,
  orderFUN = rowMeans,
  orderBy = 1,
  sampleOrder = NULL,
  groupOrder = NULL,
  fill_gradient = scale_fill_gradient(low = "blue", high = "red"),
  boderColor = NA,
  xaxis_breaks = NULL,
  xaxis_label = NULL,
  yaxis_breaks = NULL,
  yaxis_label = NULL
)

Arguments

se	a SummarizedExperiment object from importCount.
facet	This will be passed to facet_grid:rows. It can be set to NULL.
transformFUN	The transform function of values.
pseudo	Pseudo value will be add to values before apply transformFUN.
orderFUN	function used to reorder Y axis of the heatmap
orderBy	the sample name or index used to order Y axis
sampleOrder, groupOrder	order of the samples(column) or groups(row).
fill_gradient	color fill gradient function. see scale_colour_gradient.
boderColor	The color of the heatmap cell border.
xaxis_breaks, xaxis_label	xaxis breaks and labels. see scale_x_continuous.
yaxis_breaks, yaxis_label	xaxis breaks and labels. see scale_y_discrete.

Value

ggplot object

Examples

file <- system.file("extdata", "count.gz", package= "deepToolsDownstream")
se <- importCount(file)
plotHeatmap(se, yaxis_breaks="100033817", yaxis_label="geneA")