heatMapL {ORFik} | R Documentation

## 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,
      BPPARAM = bpparam()
    )

### 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?
`BPPARAM` | how many cores/threads to use? default: bpparam(). To see number of threads used, do `bpparam()$workers`. You can also add a time remaining bar, for a more detailed pipeline.

### Value

invisible(NULL), plots are saved

### See Also

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

[Package ORFik version 1.12.13 Index]