plotVariants {CrispRVariants} | R Documentation |
Combines a plot of transcript structure, alleles aligned with respect to a reference genome and a heatmap of counts or proportions of each allele in a set of data.
plotVariants(obj, ...) ## S4 method for signature 'CrisprSet' plotVariants(obj, ..., txdb = NULL, add.chr = TRUE, plotAlignments.args = list(), plotFreqHeatmap.args = list())
obj |
The object to be plotted |
... |
extra arguments for plot layout |
txdb |
GenomicFeatures:TxDb object (default: NULL) |
add.chr |
If target chromosome does not start with "chr", e.g. "chr5", add the "chr" prefix. (Default:TRUE) |
plotAlignments.args |
Extra arguments for plotAlignments |
plotFreqHeatmap.args |
Extra arguments for plotFreqHeatmap |
A ggplot2 plot of the variants
arrangePlots
for general layout options
and annotateGenePlot
for options relating
to the transcript plot.
#Load a CrisprSet object for plotting data("gol_clutch1") #Load the transcript db. This is a subset of the Ensembl Danio Rerio v73 gtf # for the region 18:4640000-4650000 which includes the targeted gol gene library(GenomicFeatures) fn <- system.file("extdata", "Danio_rerio.Zv9.73.gol.sqlite", package = "CrispRVariants") txdb <- loadDb(fn) # Plot the variants p <- plotVariants(gol, txdb = txdb) #In the above plot, the bottom margin is too large, the legend is #cut off, and the text within the plots should be larger. #These issues can be fixed with some adjustments: p <- plotVariants(gol, txdb = txdb, plotAlignments.args = list(plot.text.size = 4, legend.cols = 2), plotFreqHeatmap.args = list(plot.text.size = 4), left.plot.margin = grid::unit(c(0.1,0,0.5,1), "lines"))