heatMapRegion: Create coverage heatmaps of specified region

In JokingHero/ORFik: Open Reading Frames in Genomics

Create coverage heatmaps of specified region

Description

Simplified input space for easier abstraction of coverage heatmaps
Pick your transcript region and plot directly
Input CAGE file if you use TSS and want improved 5' annotation.

Usage

heatMapRegion(
  df,
  region = "TIS",
  outdir = "default",
  scores = c("transcriptNormalized", "sum"),
  type = "ofst",
  cage = NULL,
  plot.ext = ".pdf",
  acceptedLengths = 21:75,
  upstream = c(50, 30),
  downstream = c(29, 69),
  shifting = c("5prime", "3prime"),
  longestPerGene = TRUE,
  colors = "default",
  scale_x = 5.5,
  scale_y = 15.5,
  gradient.max = "default",
  BPPARAM = BiocParallel::SerialParam()
)

Arguments

df	an ORFik experiment
region	a character, default "TIS". The centering point for the heatmap (what is position 0, beween -50 and 50 etc), can be any combination of the set: c("TSS", "TIS", "TTS", "TES"), which are: - Transcription start site (5' end of mrna) - Translation initation site (5' end of CDS) - Translation termination site (5' end of 3' UTRs) - Transcription end site (3' end of 3' UTRs)
outdir	a character path, default: "default", saves to: file.path(QCfolder(df), "heatmaps/"), a created folder within the ORFik experiment data folder for plots. Change if you want custom location.
scores	character vector, default c("transcriptNormalized", "sum"), either of zscore, transcriptNormalized, sum, mean, median, .. see ?coverageScorings for info and more alternatives.
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"
cage	a character path to library file or a GRanges, GAlignments preloaded file of CAGE data. Only used if "TSS" is defined as region, to redefine 5' leaders.
plot.ext	a character, default ".pdf", alternative ".png"
acceptedLengths	an integer vector (NULL), the read lengths accepted. Default NULL, means all lengths accepted.
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.
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.
longestPerGene	logical, default TRUE. Use only longest transcript isoform per gene. This will speed up your computation.
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.
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(), heatMapL(), heatMap_single()

Examples

# Toy example, will not give logical output, but shows how it works
df <- ORFik.template.experiment()[9:10,] # Subset to 2 Ribo-seq libs
#heatMapRegion(df, "TIS", outdir = "default")
#
# Do also TSS, add cage for specific TSS
# heatMapRegion(df, c("TSS", "TIS"), cage = "path/to/cage.bed")

# Do on pshifted reads instead of original files
remove.experiments(df) # Remove loaded experiment first
# heatMapRegion(df, "TIS", type = "pshifted")

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