heatMapL: Coverage heatmap of multiple libraries

In ORFik: Open Reading Frames in Genomics

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,
  format = ".png",
  plot.together = TRUE,
  title = TRUE
)

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 either or NULL (no shifting of reads)
skip.last	skip top(highest) read length, default FALSE
format	a character, default ".png", alternative ".pdf"
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?

Value

invisible(NULL), plots are saved

See Also

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

ORFik documentation built on March 27, 2021, 6 p.m.