kpBars: kpBars

Description Usage Arguments Details Value See Also Examples

View source: R/kpBars.R

Description

Plot bars along the genome

Usage

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kpBars(karyoplot, data=NULL, chr=NULL, x0=NULL, x1=x0, y1=NULL, y0=NULL, ymin=NULL, ymax=NULL, data.panel=1, r0=NULL, r1=NULL, ...)

Arguments

karyoplot

(a KaryoPlot object) This is the first argument to all data plotting functions of karyoploteR. A KaryoPlot object referring to the currently active plot.

data

(a GRanges) A GRanges object with the data. If data is present, chr will be set to seqnames(data), x0 to start(data) and x1 to end(data). If no parameter y0 is specified and data has a column named y0, this column will be used. The same for y1. (defaults to NULL)

chr

(a charecter vector) A vector of chromosome names specifying the chromosomes of the data points. If data is not NULL, chr is ignored. (defaults to NULL)

x0

(a numeric vector) A numeric vector of x left positions (in base pairs). If data is not NULL, x0. (defaults to NULL)

x1

(a numeric vector) A numeric vector of x right positions (in base pairs). If data is not NULL, x1. (defaults to NULL)

y1

(a numeric vector) A numeric vector of y top positions. If y is not NULL, it is used instead of any data column in data. (defaults to NULL)

y0

(a numeric vector) A numeric vector of y bottom positions. If y is not NULL, it is used instead of any data column in data. (defaults to NULL)

ymin

(numeric) The minimum value of y to be plotted. If NULL, it is set to the min value of the selected data panel. (defaults to NULL)

ymax

(numeric) The maximum value of y to be plotted. If NULL, it is set to the max value of the selected data panel. (defaults to NULL)

data.panel

(numeric) The identifier of the data panel where the data is to be plotted. The available data panels depend on the plot type selected in the call to plotKaryotype. (defaults to 1)

r0

(numeric) 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) 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 the R base plotting functions.

Details

kpBars plots bars (rectangles) along the genome. It is very similar to kpRect except that if y0 is missing, it's automatically set to ymin so all bars start from the base of the plotting region.

Value

Returns the original karyoplot object, unchanged.

See Also

plotKaryotype, kpRect, kpLines

Examples

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set.seed(1000)

data <- toGRanges(data.frame(chr="chr1", start=10000000*(0:23), end=10000000*(1:24)))
y1 <- ((sin(start(data)) + rnorm(n=24, mean=0, sd=0.1))/5)+0.5
y0 <- y1 - rnorm(n=24, mean = 0, sd = 0.15)
 
kp <- plotKaryotype("hg19", plot.type=2, chromosomes=c("chr1", "chr2"))

#We can specify all data values separately. If missing y0, it defaults to ymin
kpBars(kp, chr=as.character(seqnames(data)), x0=start(data), x1=end(data), y1=y1,
       col="#FFBBBB", border="#EEAAAA")
kpLines(kp, data=data, y=y1, col="red")

#or we can provide all data into a single GRanges object
mcols(data) <- data.frame(y0=y0, y1=y1)
kpBars(kp, data[data$y0>data$y1], col="orange", border="orange", data.panel=2)
kpBars(kp, data[data$y0<=data$y1], col="purple", border="purple", data.panel=2)

kpLines(kp, data, y=data$y1, data.panel=2, col="red")
kpLines(kp, data, y=data$y0, data.panel=2, col="blue")

kpAxis(kp, data.panel = 1, cex=0.8, numticks = 5, col="#777777")
kpAxis(kp, data.panel = 2, cex=0.8, numticks = 5, col="#777777")

Bioconductor-mirror/karyoploteR documentation built on July 4, 2017, 6:39 p.m.