coverageHeatMap {ORFik} | R Documentation

## Create a heatmap of coverage

### Description

Coverage rows in heat map is fraction Coverage column in heat map is score, default zscore of counts

### Usage

    coverageHeatMap(coverage, output = NULL, scoring = "zscore")

### Arguments

`coverage` | a data.table, output of scaledWindowCoverage
`output` | character string (NULL), if set, saves the plot as pdf or png to path given. If no format is given, is save as pdf.
`scoring` | character vector (zscore), either of zScore, transcriptNormalized, sum, mean, median, NULL. Set NULL if already scored.

### Details

See vignette for example

### Value

a ggplot object of the coverage plot, NULL if output is set, then the plot will only be saved to location.

### See Also

Other coveragePlot: `pSitePlot`, `savePlot`, `windowCoveragePlot`

### Examples

    # An ORF
    grl <- GRangesList(tx1 = GRanges("1", IRanges(1, 6), "+"))
    # Ribo-seq reads
    range <- IRanges(c(rep(1, 3), 2, 3, rep(4, 2), 5, 6), width = 1 )
    reads <- GRanges("1", range, "+")
    reads$size <- c(rep(28, 5), rep(29, 4)) # read size
    coverage <- ORFik:::windowPerReadLength(grl, reads = reads, upstream = 0,
                                            downstream = 5)

    ORFik:::coverageHeatMap(coverage)

    # See vignette for more examples

[Package ORFik version 1.4.1 Index]