heatMap_single {ORFik} | R Documentation

## Coverage heatmap of single libraries

### Description

Coverage heatmap of single libraries

### Usage

    heatMap_single(
      region,
      tx,
      reads,
      outdir,
      scores = "sum",
      upstream,
      downstream,
      zeroPosition = upstream,
      returnCoverage = FALSE,
      acceptedLengths = NULL,
      legendPos = "right",
      colors = "default",
      addFracPlot = TRUE,
      location = "start site",
      shifting = NULL,
      skip.last = FALSE,
      title = NULL
    )

### 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"
`reads` | a `GAlignments` or `GRanges` object of RiboSeq, RnaSeq etc. Weigths for scoring is default the 'score' column in 'reads'
`outdir` | a character path to save file as: not just directory, but full name.
`scores` | character vector, default "sum", either of zscore, transcriptNormalized, sum, mean, median, .. see ?coverageScorings for info and more alternatives.
`upstream` | an integer, relative region to get upstream from.
`downstream` | an integer, relative region to get downstream from
`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.
`returnCoverage` | logical, default: FALSE, return coverage, if FALSE returns plot instead.
`acceptedLengths` | an integer vector (NULL), the read lengths accepted. Default NULL, means all lengths accepted.
`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 NULL (no shifting), can also be either of c("5prime", "3prime")
`skip.last` | skip top(highest) read length, default FALSE
`title` | a character, default NULL (no title), what is the top title of plot?

### Value

ggplot2 grob (default), data.table (if returnCoverage is TRUE)

### See Also

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

[Package ORFik version 1.10.13 Index]