Manage default colours and point characters

Source: R/environment.R

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.

setLisacol()

getLisacol()

getOldcol()

setOldcol()

getStockcol()

setStockcol(cols)

getStockpch()

setStockpch(pchs)

getUnknowncol()

setUnknowncol(col)

getUnknownpch()

setUnknownpch(pch)

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.

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

Laurent Gatto

Examples

## defaults for clusters
getStockcol()
#>  [1] "#E41A1C" "#377EB8" "#309C17" "#FF7F00" "#FFD700" "#00CED1" "#A65628"
#>  [8] "#F781BF" "#984EA3" "#9ACD32" "#B0C4DE" "#00008A" "#FDAE6B" "#EBB7BE"
#> [15] "#3F8F8F" "#CF9802" "#6A51A3" "#21E8AC" "#0000FF" "#1D7A3E" "#BF2A6B"
#> [22] "#CD5B45" "#808000" "#F21D56" "#67000D" "#7A0C79" "#93EDF5" "#A66A6A"
#> [29] "#0E438A" "#DBBCF7"
getStockpch()
#>  [1] 19  1 15  0 17  2 18  5  7  9 13  3  4  8
## unknown features
getUnknownpch()
#> [1] 21
getUnknowncol()
#> [1] "#E0E0E0"
## an example
library(pRolocdata)
data(dunkley2006)
par(mfrow = c(2, 1))
plot2D(dunkley2006, fcol = "markers", main = 'Default colours')
setUnknowncol("black")
plot2D(dunkley2006, fcol = "markers", main = 'setUnknowncol("black")')

getUnknowncol()
#> [1] "black"
setUnknowncol(NULL)
getUnknowncol()
#> [1] "#E0E0E0"
getStockcol()
#>  [1] "#E41A1C" "#377EB8" "#309C17" "#FF7F00" "#FFD700" "#00CED1" "#A65628"
#>  [8] "#F781BF" "#984EA3" "#9ACD32" "#B0C4DE" "#00008A" "#FDAE6B" "#EBB7BE"
#> [15] "#3F8F8F" "#CF9802" "#6A51A3" "#21E8AC" "#0000FF" "#1D7A3E" "#BF2A6B"
#> [22] "#CD5B45" "#808000" "#F21D56" "#67000D" "#7A0C79" "#93EDF5" "#A66A6A"
#> [29] "#0E438A" "#DBBCF7"
getOldcol()
#>  [1] "#E41A1C" "#377EB8" "#4DAF4A" "#984EA3" "#FF7F00" "#FFFF33" "#A65628"
#>  [8] "#F781BF" "#999999" "#333333" "#A021EF" "#008A45" "#00008A"