plotHist {strandCheckR} | R Documentation |
Plot the histogram of positive proportions of the input histogram data frame
plotHist(windows, save = FALSE, file = "hist.pdf", group_by = NULL, normalize_by = NULL, split = c(10, 100, 1000), breaks = 100, useCoverage = FALSE, heatmap = FALSE, ...)
windows |
data frame containing the strand information of the sliding
windows. Windows can be obtained using the function |
save |
if TRUE, then the plot will be save into the file given by
|
file |
the file name to save to plot |
group_by |
the column names of windows that will be used to group the data |
normalize_by |
the column names of windows that will be used to normalize the read count or read coverage into proportion |
split |
an integer vector that specifies how you want to partition the
windows based on the coverage. By default |
breaks |
an integer giving the number of bins for the histogram |
useCoverage |
if TRUE then plot the coverage strand information, otherwise plot the number of reads strand information. FALSE by default |
heatmap |
if TRUE, then use heat map to plot the histogram, otherwise use barplot. FALSE by default. |
... |
used to pass parameters to facet_wrap |
If heatmap=FALSE
: a ggplot object
bamfilein = system.file('extdata','s1.sorted.bam',package = 'strandCheckR') win <- getWinFromBamFile(file = bamfilein,sequences='10') plotHist(win)