plotEnrichedHeatmaps: plotEnrichedHeatmaps: Plots heatmaps of signals around a set...

In ETHZ-INS/epiwraps: epiwraps: Wrappers for plotting and dealing with epigenomics data

plotEnrichedHeatmaps: Plots heatmaps of signals around a set of regions

Description

Plots enrichment heatmaps from the output of signal2Matrix (i.e. an EnrichmentSE object or a list of signal matrices). This is a convenience wrapper around EnrichedHeatmap.

Usage

plotEnrichedHeatmaps(
  ml,
  trim = c(0.02, 0.98),
  assay = 1L,
  colors = NULL,
  scale_title = "density",
  column_title = NULL,
  multiScale = NULL,
  column_title_gp = gpar(fontsize = 11),
  row_order = NULL,
  cluster_rows = FALSE,
  row_split = NULL,
  axis_name = NULL,
  minRowVal = 0,
  scale_rows = FALSE,
  top_annotation = TRUE,
  left_annotation = NULL,
  right_annotation = NULL,
  mean_color = "red",
  mean_scale_side = NULL,
  mean_trim = TRUE,
  show_heatmap_legend = TRUE,
  use_raster = NULL,
  ...
)

Arguments

ml	A named matrix list as produced by signal2Matrix, or an 'EnrichmentSE' object.
trim	The quantile above which to trim values for the colorscale. If a numeric vector of length 2, will be used as lower and upper quantiles beyond which to trim.
assay	Assay to use (ignored unless 'ml' is an ESE object)
colors	The heatmap colors to use, a vector of at least two colors between which to interpolate. Can also be a list of such color scales, with as many slots as there are tracks in 'ml'. If a list of single colors, a color scale from white to that color will be used for each track. Defaults to the 'inferno' viridis palette.
scale_title	The title of the scale. Ignored if 'multiScale=TRUE'.
multiScale	Logical; whether to use a different scale for each track. Defaults to TRUE is 'colors' is a list, otherwise FALSE.
column_title_gp	Graphic parameters of the column titles (see gpar)
row_order	Optional order of the rows.
cluster_rows	Logical; whether to cluster rows. Alternatively, 'cluster_rows="sort"' will sort rows using the angle on an MDS based on the enriched_score of the signals (can be very long to compute on large matrices). 'cluster_rows=FALSE' (default) results in the traditional sorting by decreasing 'enriched_score'.
row_split	Variable according to which the rows should be split. This should either be the name of a column of 'rowData(ml)', or a factor/ character vector of length equal to the number of regions in 'ml'.
axis_name	A vector of length 3 giving the labels to put respectively on the left, center and right of the x axis of each heatmap.
minRowVal	Minimum value a row should have to be included
scale_rows	Whether to scale rows, either FALSE (default), 'local' (scales each matrix separately) or 'global'.
top_annotation	Either a logical indicating whether or not to plot the summary profile at the top of each heatmap, a named list of parameters to be passed to 'anno_enrich', or a HeatmapAnnotation-class object that will be passed to EnrichedHeatmap. Additionally, if 'ml' is a 'ESE' object, 'top_annotation' can be a vector of colData column names.
left_annotation	Passed to EnrichedHeatmap
right_annotation	Passed to EnrichedHeatmap
mean_color	Color of the mean signal line in the top annotation. If 'row_split' is used, 'mean_color' can be a named vector indicating the colors for each cluster. Can also be a 'gpar' object.
mean_scale_side	The side on which to show the y-axis scale of the mean plots. Either "both" (default), "left", "right", or "none".
mean_trim	Logical; whether to apply the trimming also to the mean plot.
show_heatmap_legend	Logical, whether to show the heatmap legend
use_raster	Logical; whether to render the heatmap body as a raster image. Turned on by default if any of the matrix dimensions is greater than 1500.
...	Passed to EnrichedHeatmap

Details

When plotting large matrices, the heatmap body will be rasterized to keep its memory footprint decent. For this to work well, make sure the 'magick' package is installed. Depending on your settings, if the heatmap is very big you might hit the preset limits of 'magick' base rasterization, which could result in an error such as 'Image must have at least 1 frame to write a bitmap'. In such cases, you might have to degrade to a lower-quality rasterization using the additional arguments 'raster_by_magick=FALSE, raster_device="CairoJPEG"' . Alternatively, the best solution is to increase the size and memory limits in the 'policy.xml' configuration of the underlying (non-R) imagemagick library.

Value

A HeatmapList object

Examples

# we first load an example EnrichmentSE, as produced by signal2Matrix:
data(exampleESE)
plotEnrichedHeatmaps(exampleESE)
# we could also just plot one with:
# plotEnrichedHeatmaps(exampleESEm[,1])
# or change the aesthetics, e.g.:
plotEnrichedHeatmaps(exampleESE, trim=0.98, scale_title="RPKM", 
                     colors=c("white","darkred"), row_title="My regions")
# any argument accepted by `EnrichedHeatmap` (and hence by 
# `ComplexHeatmap::Heatmap`) can be used.

ETHZ-INS/epiwraps documentation built on Dec. 22, 2024, 4:05 a.m.