getStockcol: Manage default colours and point characters

In lgatto/pRoloc: A unifying bioinformatics framework for spatial proteomics

Manage default colours and point characters

Description

These functions allow to get/set the colours and point character that are used when plotting organelle clusters and unknown features. These values are parametrised at the session level. Two palettes are available: the default palette (previously Lisa's colours) containing 30 colours and the old (original) palette, containing 13 colours.

Usage

setLisacol()

getLisacol()

getOldcol()

setOldcol()

getStockcol()

setStockcol(cols)

getStockpch()

setStockpch(pchs)

getUnknowncol()

setUnknowncol(col)

getUnknownpch()

setUnknownpch(pch)

getStockbg()

setStockbg(bg)

getUnknownbg()

setUnknownbg(bg)

Arguments

cols	A vector of colour characters or NULL, which sets the colours to the default values.
pchs	A vector of numeric or NULL, which sets the point characters to the default values.
col	A colour character or NULL, which sets the colour to #E7E7E7 (grey91), the default colour for unknown features.
pch	A numeric vector of length 1 or NULL, which sets the point character to 21, the default.
bg	A colour character or NULL, which sets the background (fill) colour for open plot symbols given by pch = 21:25 to the default colour for unknown features.

Value

The set functions set (and invisibly returns) colours. The get functions returns a character vector of colours. For the pch functions, numerics rather than characters.

Author(s)

Laurent Gatto

Examples

## defaults for clusters
getStockcol()
getStockbg()
getStockpch()
## unknown features
getUnknowncol()
getUnknownbg()
getUnknownpch()
## an example
library(pRolocdata)
data(dunkley2006)
par(mfrow = c(2, 1))
plot2D(dunkley2006, fcol = "markers", main = 'Default colours')
setUnknowncol("black")
setUnknownbg("grey")
plot2D(dunkley2006, fcol = "markers", 
      main = 'setUnknowncol("black") and setUnknownbg("grey")')
getUnknowncol()
getUnknownbg()
setUnknowncol(NULL)
setUnknownbg(NULL)
getUnknowncol()
getStockcol()
getOldcol()

lgatto/pRoloc documentation built on June 14, 2025, 7:56 p.m.