plotHeatmap: plot heatmap

Description Usage Arguments Value Examples

View source: R/plotHeatmap.R

Description

Plot a heatmap for counts.

Usage

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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

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

jianhong/deepToolsDownstream documentation built on Oct. 22, 2021, 7:48 a.m.