heatMapL: Coverage heatmap of multiple libraries

Description Usage Arguments Value See Also

View source: R/coverage_heatmaps.R

Description

Coverage heatmap of multiple libraries

Usage

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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.