heatMapL: Coverage heatmap of multiple libraries

In JokingHero/ORFik: Open Reading Frames in Genomics

Coverage heatmap of multiple libraries

Description

Coverage heatmap of multiple libraries

Usage

heatMapL(
  region,
  tx,
  df,
  outdir,
  scores = "sum",
  upstream,
  downstream,
  zeroPosition = upstream,
  acceptedLengths = NULL,
  type = "ofst",
  legendPos = "right",
  colors = "default",
  addFracPlot = TRUE,
  location = "TIS",
  shifting = NULL,
  skip.last = FALSE,
  plot.ext = ".pdf",
  plot.together = TRUE,
  title = TRUE,
  scale_x = 5.5,
  scale_y = 15.5,
  gradient.max = "default",
  BPPARAM = BiocParallel::SerialParam()
)

Arguments

region	#' a GRangesList object of region, usually either leaders, cds', 3' utrs or ORFs, start region, stop regions etc. This is the region that will be mapped in heatmap
tx	default NULL, a GRangesList of transcripts or (container region), names of tx must contain all grl names. The names of grl can also be the ORFik orf names. that is "txName_id"
df	an ORFik experiment
outdir	a character path to directory to save plot, will be named from ORFik experiment columns
scores	character vector, default c("transcriptNormalized", "sum"), either of zscore, transcriptNormalized, sum, mean, median, .. see ?coverageScorings for info and more alternatives.
upstream	1 or 2 integers, default c(50, 30), how long upstream from 0 should window extend (first index is 5' end extension, second is 3' end extension). If only 1 shifting, only 1 value should be given, if two are given will use first.
downstream	1 or 2 integers, default c(29, 69), how long upstream from 0 should window extend (first index is 5' end extension, second is 3' end extension). If only 1 shifting, only 1 value should be given, if two are given will use first.
zeroPosition	an integer DEFAULT (upstream), what is the center point? Like leaders and cds combination, then 0 is the TIS and -1 is last base in leader. NOTE!: if windows have different widths, this will be ignored.
acceptedLengths	an integer vector (NULL), the read lengths accepted. Default NULL, means all lengths accepted.
type	character, default: "ofst". Type of library: either "default", usually bam format (the one you gave to experiment), "pshifted" pshifted reads, "ofst", "bed", "bedo" optimized bed, or "wig"
legendPos	a character, Default "right". Where should the fill legend be ? ("top", "bottom", "right", "left")
colors	character vector, default: "default", this gives you: c("white", "yellow2", "yellow3", "lightblue", "blue", "navy"), do "high" for more high contrasts, or specify your own colors.
addFracPlot	Add margin histogram plot on top of heatmap with fractions per positions
location	a character, default "start site", will make xlabel of heatmap be Position relative to "start site" or alternative given.
shifting	a character, default c("5prime", "3prime"), can also be NULL (no shifting of reads). If NULL, will use first index of 'upstream' and 'downstream' argument.
skip.last	skip top(highest) read length, default FALSE
plot.ext	a character, default ".pdf", alternative ".png"
plot.together	logical (default: FALSE), plot all in 1 plot (if TRUE)
title	a character, default NULL (no title), what is the top title of plot?
scale_x	numeric, how should the width of the single plots be scaled, bigger the number, the bigger the plot
scale_y	numeric, how should the height of the plots be scaled, bigger the number, the bigger the plot
gradient.max	numeric or character, default: "default", which is: max(coverage$score), the max coverage over all readlengths. If you want all plots to use same reference point for max scaling, then first detect this point, look at max in plot etc, and use that value, to get all plots to have same max point.
BPPARAM	a core param, default: single thread: BiocParallel::SerialParam(). Set to BiocParallel::bpparam() to use multicore. Be aware, this uses a lot of extra ram (40GB+) for larger human samples!

Value

invisible(NULL), plots are saved

See Also

Other heatmaps: coverageHeatMap(), heatMapRegion(), heatMap_single()

JokingHero/ORFik documentation built on Dec. 21, 2024, 12:01 a.m.