GENOVA_image: Display a part of a Hi-C matrix

In robinweide/GENOVA: GENOVA: expore the Hi-C

Display a part of a Hi-C matrix

Description

Display a part of a Hi-C matrix

Usage

## S3 method for class 'contacts_matrix'
image(x, col = NULL, zlim = NULL, xlab = NULL, ylab = NULL, ...)

Arguments

x	A contacts_matrix object, as returned by select_subset().
col	a list of colors such as that generated by hcl.colors, gray.colors or similar functions. Defaults to GENOVA palette.
zlim	the minimum and maximum z values for which colors should be plotted, defaulting to the range of finite values of off-diagonal elements of x.
xlab, ylab	each a character string giving the labels for the x and y axis. Default is to use the chromosome name as axis title.
...	Arguments passed on to graphics::image.default xlim,ylim ranges for the plotted x and y values, defaulting to the ranges of x and y. add logical; if TRUE, add to current plot (and disregard the following four arguments). This is rarely useful because image ‘paints’ over existing graphics. xaxs,yaxs style of x and y axis. The default "i" is appropriate for images. See par. xlab,ylab each a character string giving the labels for the x and y axis. Default to the ‘call names’ of x or y, or to "" if these were unspecified. breaks a set of finite numeric breakpoints for the colours: must have one more breakpoint than colour and be in increasing order. Unsorted vectors will be sorted, with a warning. oldstyle logical. If true the midpoints of the colour intervals are equally spaced, and zlim[1] and zlim[2] were taken to be midpoints. The default is to have colour intervals of equal lengths between the limits. useRaster logical; if TRUE a bitmap raster is used to plot the image instead of polygons. The grid must be regular in that case, otherwise an error is raised. For the behaviour when this is not specified, see ‘Details’.

Examples

## Not run: 
x <- select_subset(exp, "chr1", 50e6, 60e6)
image(x)

## End(Not run)

robinweide/GENOVA documentation built on March 14, 2024, 11:16 p.m.