plotStackProfile {epistack} | R Documentation |
Display a heatmap of an epigenetic track centered at genomic anchors such as Transcription Start Sites or peak center.
plotStackProfile( gr, pattern = "^window_", x_labels = c("Before", "Anchor", "After"), title = "", zlim = NULL, palette = function(n) viridisLite::viridis(n, direction = -1), target_height = 650, summary_func = function(x) mean(x, na.rm = TRUE), n_core = 1 )
gr |
a GRanges input |
pattern |
a character vector of length 1 of a column prefixe
(can be regular expressions) that should match columns of |
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 |
n_core |
multicore option, passed to |
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 GRanges
used as an input (hereafter gr
).
Anchors are plotted from top to bottom in the same order as in gr
.
One should sort gr
before plotting if needed.
The matrix used to display the heatmap should be passed as
additional metadata columns of gr
. Such matrix can be obtained using
EnrichedHeatmap::normalizeToMatrix()
for example. The matrix columns
names are then specified through what_pattern
using a prefix, a suffix
or a regular expressions.
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()
.
Display a plot.
plotAverageProfile
,
plotEpistack
,
normalizeToMatrix
,
plotStackProfileLegend
data("stackepi") plotStackProfile(stackepi, target_height = 650, zlim = c(0, 1), palette = colorRampPalette(c("white", "dodgerblue", "black")), title = "DNA methylation")