| coverageHeatMap {ORFik} | R Documentation |
Coverage rows in heat map is fraction Coverage column in heat map is score, default zscore of counts
coverageHeatMap(coverage, output = NULL, scoring = "zscore")
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. |
See vignette for example
a ggplot object of the coverage plot, NULL if output is set, then the plot will only be saved to location.
Other coveragePlot: pSitePlot,
savePlot, windowCoveragePlot
# 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