pSitePlot {ORFik} | R Documentation |
Usefull to validate p-shifting is correct Can be used for any coverage of region around a point, like TIS, TSS, stop site etc.
pSitePlot( hitMap, length = 29, region = "start", output = NULL, type = "canonical CDS", scoring = "Averaged counts", forHeatmap = FALSE )
hitMap |
a data.frame/data.table, given from metaWindow (must have columns: position, (score or count) and frame) |
length |
an integer (29), which length is this for? |
region |
a character (start), either "start or "stop" |
output |
character (NULL), if set, saves the plot as pdf or png to path given. If no format is given, is save as pdf. |
type |
character (canonical CDS), type for plot |
scoring |
character, default: (Averaged counts), which scoring did you use ? see ?coverageScorings for info and more alternatives. |
forHeatmap |
a logical (FALSE), should the plot be part of a heatmap? It will scale it differently. Removing title, x and y labels, and truncate spaces between bars. |
The region is represented as a histogram with different colors for the 3 frames. To make it easy to see patterns in the reads. Remember if you want to change anything like colors, just return the ggplot object, and reassign like: obj + scale_color_brewer() etc.
a ggplot object of the coverage plot, NULL if output is set, then the plot will only be saved to location.
Other coveragePlot:
coverageHeatMap()
,
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, "+") coverage <- coveragePerTiling(grl, reads, TRUE, as.data.table = TRUE, withFrames = TRUE) pSitePlot(coverage) # See vignette for more examples