plotAssayHeatmap-methods: Draw a heatmap from a single SummarizedExperiment assay

In steveped/extraChIPs: Additional functions for working with ChIP-Seq data

Draw a heatmap from a single SummarizedExperiment assay

Description

Use ggplot2 to create a heatmap from a SummarizedExperiment object

Usage

plotAssayHeatmap(x, ...)

## S4 method for signature 'SummarizedExperiment'
plotAssayHeatmap(
  x,
  assay = "counts",
  by_x = "colnames",
  facet_x = NULL,
  ysideline = FALSE,
  yside_col = NULL,
  trans = NULL,
  n_max = 100,
  ...
)

Arguments

x	a SummarizedExperiment object
...	Not used
assay	the assay to take values from
by_x	the parameter to use for the x-axis. Will default to column names but should be one value per sample, such as an additional column containing shortened sample labels.
facet_x	column from colData(x) which will be used to group samples along the x-axis
ysideline	logical(1) Draw a line across the side of the y-axis summarising values for each range
yside_col	column from colData(x) to group and colour the lines drawn on the side of the y-axis. If grouping by treatment or replicate, the mean values will be shown
trans	character(1). Any transformative function to be applied to the data before calculating the density, e.g. trans = "log2"
n_max	Maximum number of ranges to draw

Details

Draw a heatmap containing selected values from an assay within a SummarizedExperiment object. Columns within the colData element of the object can be used to facet along the x-axis (e.g. treatment groups). The maximum number of points is set to be 100, although this can be changed easily should the plot require more ranges to be drawn.

The averages across any grouping of samples can be drawn as a line plot on the side of the y-axis by setting ysideline = TRUE, with groups as specified in yside_col. This feature is added for the specific context of neighbouring or overlapping ranges, and as such may be less informative in any other scenario

The returned object is a ggplot2 object so scales can easily be added after heatmap creation using scale_fill_\* for the main heatmap, and scale_colour_\* for any groupings along the y-axis

Value

A ggplot2 object. Scales and labels can be added using conventional ggplot2 syntax.

Examples

nrows <- 10; ncols <- 4
counts <- matrix(runif(nrows * ncols, 1, 1e4), nrows)
colnames(counts) <- paste0("Sample_", seq_len(ncols))
df <- DataFrame(treat = c("A", "A", "B", "B"))
se <- SummarizedExperiment(
  assays = SimpleList(counts = counts),
  colData = df
)
rowRanges(se) <- GRanges(paste0("chr1:", seq_len(nrows)))
plotAssayHeatmap(se, facet_x = "treat")

steveped/extraChIPs documentation built on Aug. 1, 2024, 12:36 a.m.