plot_discovery: Plot discoveries

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

Plot discoveries

Description

The base R plotting equivalent to visualise for discovery objects.

Usage

## S3 method for class 'APA_discovery'
plot(
  x,
  contrast = 1,
  colour_fun = NULL,
  colour_fun_contrast = NULL,
  colour_lim = NULL,
  colour_lim_contrast = NULL,
  ...
)

## S3 method for class 'CSCAn_discovery'
plot(x, colour_fun = NULL, colour_lim = NULL, ...)

## S3 method for class 'PESCAn_discovery'
plot(
  x,
  contrast = 1,
  colour_fun = NULL,
  colour_fun_contrast = NULL,
  colour_lim = NULL,
  colour_lim_contrast = NULL,
  ...
)

## S3 method for class 'ATA_discovery'
plot(
  x,
  contrast = 1,
  colour_fun = NULL,
  colour_fun_contrast = NULL,
  colour_lim = NULL,
  colour_lim_contrast = NULL,
  ...
)

## S3 method for class 'ARA_discovery'
plot(
  x,
  contrast = 1,
  colour_fun = NULL,
  colour_fun_contrast = NULL,
  colour_lim = NULL,
  colour_lim_contrast = NULL,
  ...
)

## S3 method for class 'CS_discovery'
plot(x, chr = "chr1", start = NULL, end = NULL, contrast = NULL, ...)

## S3 method for class 'IS_discovery'
plot(x, chr = "chr1", start = NULL, end = NULL, contrast = NULL, ...)

## S3 method for class 'DI_discovery'
plot(x, chr = "chr1", start = NULL, end = NULL, contrast = NULL, ...)

## S3 method for class 'saddle_discovery'
plot(
  x,
  contrast = 1,
  colour_fun = NULL,
  colour_fun_contrast = NULL,
  colour_lim = NULL,
  colour_lim_contrast = NULL,
  ...
)

## S3 method for class 'domainogram_discovery'
plot(x, colour_fun = NULL, colour_lim = c(-1, 1), minimalist = FALSE, ...)

## S3 method for class 'RCP_discovery'
plot(x, contrast = 1, metric = c("smooth"), ...)

## S3 method for class 'virtual4C_discovery'
plot(x, censor_vp = TRUE, ...)

## S3 method for class 'IIT_discovery'
plot(
  x,
  contrast = 1,
  censor_contrast = TRUE,
  geom = c("boxplot", "point"),
  ...
)

Arguments

x	A discovery object.
contrast	An integer or character matching an experiment (name) of length 1, specifying which sample should be used to make a contrast with all other samples. Alternatively, set to NULL to not plot contrast panels.
colour_fun, colour_fun_contrast	A function that takes an integer as input and returns colours as output, to colour raster-like data or the constrast panels of raster-like data. Typically a function generated by colorRampPalette.
colour_lim, colour_lim_contrast	A numeric of length 2 indicating the minimum and maximum values for which colours should be plotted.
...	Not currently used for discovery plots.
chr	A character vector of length 1 with the name of a chromosome.
start	An integer of length 1 with the start basepair of the region to be plotted.
end	An integer of length 1 with the ending basepair of the region to be plotted.
minimalist	[domainogram] A logical of length 1. If TRUE, plot only the first experiment in the discovery and don't plot any axis, titles or legends.
metric	[RCP] Currently not in use.
censor_vp	[virtual_4C] A logical of length 1 deciding wether the values underneath the viewpoint should be excluded.
censor_contrast	[IIT] A logical of length 1 deciding wether the contrasting experiment itself should be censored (TRUE) or included (FALSE).
geom	A character of length 1 indicating what geometry should be plotted. Either "boxplot" or "point".

Value

Nothing, but outputs a plot to the graphics device.

Examples

## Not run: 
plot(discovery)

## End(Not run)

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