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 1.4.0 Index]