rc.plot.histogram {NetWeaver}

Plot Histogram, Barchart or Heat-map

Description

Add a track of histogram, barchart, or heat-map on a circos plot.

Usage

rc.plot.histogram(Data, track.id, data.col=NULL, color.col=NULL,
 color.gradient=NULL, fixed.height=FALSE, track.color=NA, track.border=NULL,
 polygon.border=NULL, custom.track.height=NULL, max.value=NULL)

Arguments

Data

data.frame, data to be plotted. See Details.

track.id

integer, in which track to plot.

data.col

integer, specifying the column that contains the data for plotting.

color.col

integer, specifying the column that contains the color.

color.gradient

a vector of gradient colors. See details.

fixed.height

logical, whether to fix the histogram height which results in heat-map. TRUE if data.col is bar.color.

track.color

NA or color code for the track background.

track.border

the color to draw the track border. Use NA to omit borders.

polygon.border

the color to draw the polygon border. See explanation for polygon.

custom.track.height

NULL or numeric, specifying customized track height to overwrite the default. See rc.get.params for default value.

max.value

NULL or numeric, specifying the maximum data value for normalization. Default NULL, get max from data column.

Details

Data must have at least three columns. The first three columns must be named as Chr, Start and End, specifying the chromosomes and positions for the start and end points of the links. Additional columns can be used to specify data and color.

If color.gradient is not NULL, color.col is ignored and the data will be scaled to positive integers in the range of 1~length(color.gradient) to index the colors in vector color.gradient.

For plotting stacked barcharts, use function rc.plot.barchart instead.

Author(s)

Minghui Wang <[e-mail]>

See Also

rc.plot.link, rc.plot.mHistogram, rc.plot.barchart

Examples

#This is not to be run alone. Please see tutorial vignette("netweaver") for usage.