plotCopyNumberSummary: plotCopyNumberSummary

In bernatgel/CopyNumberPlots: Create Copy-Number Plots using karyoploteR functionality

plotCopyNumberSummary

Description

Plot a summary of copy number status over a number of samples using a histogram-like representation.

Usage

plotCopyNumberSummary(karyoplot, cn.calls, direction="in",  gain.color=NULL, normal.color=NULL, loss.color=NULL, add.grid=FALSE, grid.color="white", labels=NULL, label.cex=1, label.srt=0, pos=2, r0=0, r1=1, ...)

Arguments

karyoplot	(a KaryoPlot object) The object returned by the plotKaryotype function and representing the current active plot.
cn.calls	(a list of GRanges or a GRangesList) A list of GRanges or a GRangesList containing the GRanges objects with cn.column value
direction	The direction to which the coverage plot point, either "in" for inward or "out" for outward. (defaults to "in")
gain.color	(color) The color assigned to gains (defaults to NULL)
normal.color	(color) The color assigned to normal ploidy(defaults to NULL)
loss.color	(colors) The color assigned to losses(defaults to NULL)
add.grid	(logical) Whether to add lines as a grid in the plot (defaults to FALSE)
grid.color	(color) The color of the grid (defaults to "white")
labels	(a character) The text of the label to identify the data. If NA, no label will be plotted. If NULL, if snps is a single sample GRanges it will default to "CN", if it's a list of samples it will default to the names in the list or consecutive numbers if names(snps) is NULL. (defaults to NULL)
label.cex	(numeric) The size of the label (defaults to 1.5)
label.srt	(numeric) The rotation of the label (defaults to 90, vertical text)
pos	The position of the label (defaults to 2)
r0	(numeric) (karyoploteR parameter) r0 and r1 define the vertical range of the data panel to be used to draw this plot. They can be used to split the data panel in different vertical ranges (similar to tracks in a genome browser) to plot differents data. If NULL, they are set to the min and max of the data panel, it is, to use all the available space. (defaults to NULL)
r1	(numeric) (karyoploteR parameter) r0 and r1 define the vertical range of the data panel to be used to draw this plot. They can be used to split the data panel in different vertical ranges (similar to tracks in a genome browser) to plot differents data. If NULL, they are set to the min and max of the data panel, it is, to use all the available space. (defaults to NULL)
...	The ellipsis operator can be used to specify any additional graphical parameters. Any additional parameter will be passed to the internal calls to karyoploteR functions.

Details

2 types of plots. Convergent or divergent barplots

Value

Invisibly returns the karyoplot object representing the plot. With it it is possible to add other elements to the plot using standrad karyoploteR functions

Examples

all.scnas <- list(
             loadCopyNumberCalls(system.file("extdata", "S1.segments.txt", package = "CopyNumberPlots", mustWork = TRUE)),
             loadCopyNumberCalls(system.file("extdata", "S2.segments.txt", package = "CopyNumberPlots", mustWork = TRUE)),
             loadCopyNumberCalls(system.file("extdata", "S3.segments.txt", package = "CopyNumberPlots", mustWork = TRUE))
             )
             
kp <- plotKaryotype(chromosomes="chr1")
#plotCopyNumberCalls(kp, all.scnas, r0=0.4, r1=1)
#plotCopyNumberSummary(kp, all.scnas, r0=0, r1=0.35)

kp <- plotKaryotype(chromosomes="chr1")
#plotCopyNumberSummary(kp, all.scnas, gain.col="blue", loss.col="red", labels="Copy Number", r0=0, r1=0.3, label.srt=90, pos=3)
#plotCopyNumberSummary(kp, all.scnas, direction="out", add.grid=TRUE, r0=0.35, r1=0.65)
#plotCopyNumberSummary(kp, all.scnas, direction="out", r0=0.7, r1=1)
kpAxis(kp, ymin=0, ymax=10, r0=0.85, r1=1, tick.pos = c(0,5,10))
kpAxis(kp, ymin=0, ymax=10, r0=0.85, r1=0.7, tick.pos = c(5,10))


#NOT RUN (time constraints in Bioconductor checks): 
# Use a random example with more realistic results
# gg <- filterChromosomes(getGenome("hg19"))

# all.scnas <- list()
# for(i in seq_len(10)) {
#   scnas <- createRandomRegions(40, 10e6, 10e6)
#   scnas$cn <- floor(runif(40, 0, 4))
#   scnas$loh <- ifelse(scnas$cn<2, 1, 0)
#   normal.regs <- subtractRegions(gg, scnas)
#   normal.regs$cn <- 2
#   scnas <- sort(c(scnas, normal.regs))
#   all.scnas[[paste0("samp", i)]] <- scnas
# }

# kp <- plotKaryotype("hg19", plot.type=4)
# plotCopyNumberSummary(kp, all.scnas)

# kp <- plotKaryotype("hg19", plot.type=4)
# plotCopyNumberSummary(kp, all.scnas, gain.col="blue", loss.col="red", labels="Copy Number", r0=0, r1=0.3, label.srt=90, pos=3)
# plotCopyNumberSummary(kp, all.scnas, direction="out", add.grid=TRUE, r0=0.35, r1=0.65)
# plotCopyNumberSummary(kp, all.scnas, direction="out", r0=0.7, r1=1)
# kpAxis(kp, ymin=0, ymax=10, r0=0.85, r1=1, tick.pos = c(0,5,10))
# kpAxis(kp, ymin=0, ymax=10, r0=0.85, r1=0.7, tick.pos = c(5,10))

bernatgel/CopyNumberPlots documentation built on Sept. 22, 2023, 1:53 a.m.