plotStackProfile: plotStackProfile()
In GenEpi-GenPhySE/epistack: Heatmaps of Stack Profiles from Epigenetic Signals

plotStackProfile

R Documentation

plotStackProfile()

Description

Display a heatmap of an epigenetic track centered at genomic anchors such as Transcription Start Sites or peak center.

Usage

plotStackProfile(
  rse,
  assay = NULL,
  x_labels = c("Before", "Anchor", "After"),
  title = "",
  zlim = NULL,
  palette = function(n) grDevices::hcl.colors(n, rev = TRUE),
  target_height = 650,
  summary_func = function(x) mean(x, na.rm = TRUE),
  n_core = 1,
  pattern = NULL
)

Arguments

`rse`	a RangedSummarizedExperiment input. Aletrnatively: can be a GRanges object (for backward compatibility, `pattern` will be required).
`assay`	specify the name of the assay to plot, that should match one of `assayNames(rse)`.
`x_labels`	a character vectors of length 3 used to label the x-axis.
`title`	The title of the heatmap
`zlim`	The minimum and maximum z values to match color to values. Format: zlim = c (min, max)
`palette`	a palette of color, (i.e. a function of parameter n that should retrun n colors).
`target_height`	The matrix height is reduced to this number of rows before plotting. Useful to limit overplotting artefacts. It should roughtly be set to the pixel height in the final heatmap.
`summary_func`	function passed to `redimMatrix()`. Usualy `mean`, but can be set to `median` or `max` for sparse matrices.
`n_core`	multicore option, passed to `redimMatrix()`.
`pattern`	only if `rse` is of class GRanges. A character vector of length 1 of a column prefixe (can be regular expressions) that should match columns of `rse`.

Details

The visualisation is centered on an anchor, a set of genomic coordinated that can be transcription start sites or peak center for example. Anchor coordinates are those of the RangedSummarizedExperiment object used as an input (hereafter rse).

Anchors are plotted from top to bottom in the same order as in rse. One should sort rse before plotting if needed.

The matrix used to display the heatmap should be passed as assay of rse. Such matrix can be obtained using EnrichedHeatmap::normalizeToMatrix() for example.

This function scale reasonnably wells up to hundred thousands of regions. Overplotting issues are solved by last-minute reduction of the matrix size using redimMatrix().

Value

Display a plot.

Examples

data("stackepi")
plotStackProfile(stackepi,
                   target_height = 650,
                   zlim = c(0, 1),
                   palette = colorRampPalette(c("white", "dodgerblue", "black")),
                   title = "DNA methylation")

GenEpi-GenPhySE/epistack documentation built on July 27, 2023, 1:09 a.m.