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.
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(s)
Laurent Gatto
Examples
## defaults for clusters
getStockcol()
getStockpch()
## unknown features
getUnknownpch()
getUnknowncol()
## 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()
setUnknowncol(NULL)
getUnknowncol()
getStockcol()
getOldcol()
Results
R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
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> library(pRoloc)
Loading required package: MSnbase
Loading required package: BiocGenerics
Loading required package: parallel
Attaching package: 'BiocGenerics'
The following objects are masked from 'package:parallel':
clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
clusterExport, clusterMap, parApply, parCapply, parLapply,
parLapplyLB, parRapply, parSapply, parSapplyLB
The following objects are masked from 'package:stats':
IQR, mad, xtabs
The following objects are masked from 'package:base':
Filter, Find, Map, Position, Reduce, anyDuplicated, append,
as.data.frame, cbind, colnames, do.call, duplicated, eval, evalq,
get, grep, grepl, intersect, is.unsorted, lapply, lengths, mapply,
match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank,
rbind, rownames, sapply, setdiff, sort, table, tapply, union,
unique, unsplit
Loading required package: Biobase
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
Loading required package: mzR
Loading required package: Rcpp
Loading required package: BiocParallel
Loading required package: ProtGenerics
This is MSnbase version 1.20.7
Read '?MSnbase' and references therein for information
about the package and how to get started.
Attaching package: 'MSnbase'
The following object is masked from 'package:stats':
smooth
The following object is masked from 'package:base':
trimws
Loading required package: MLInterfaces
Loading required package: annotate
Loading required package: AnnotationDbi
Loading required package: stats4
Loading required package: IRanges
Loading required package: S4Vectors
Attaching package: 'S4Vectors'
The following objects are masked from 'package:base':
colMeans, colSums, expand.grid, rowMeans, rowSums
Loading required package: XML
Loading required package: cluster
This is pRoloc version 1.12.4
Read '?pRoloc' and references therein for information
about the package and how to get started.
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/pRoloc/getStockcol.Rd_%03d_medium.png", width=480, height=480)
> ### Name: setLisacol
> ### Title: Manage default colours and point characters
> ### Aliases: getLisacol getOldcol getStockcol getStockpch getUnknowncol
> ### getUnknownpch setLisacol setOldcol setStockcol setStockpch
> ### setUnknowncol setUnknownpch
>
> ### ** Examples
>
> ## defaults for clusters
> getStockcol()
[1] "#E41A1C" "#377EB8" "#238B45" "#FF7F00" "#FFD700" "#333333" "#00CED1"
[8] "#A65628" "#F781BF" "#984EA3" "#9ACD32" "#B0C4DE" "#00008A" "#8B795E"
[15] "#FDAE6B" "#66C2A5" "#276419" "#CD8C95" "#6A51A3" "#EEAD0E" "#0000FF"
[22] "#9ACD32" "#CD6090" "#CD5B45" "#8E0152" "#808000" "#67000D" "#3F007D"
[29] "#6BAED6" "#FC9272"
> 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)
This is pRolocdata version 1.10.0.
Use 'pRolocdata()' to list available data sets.
> 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" "#238B45" "#FF7F00" "#FFD700" "#333333" "#00CED1"
[8] "#A65628" "#F781BF" "#984EA3" "#9ACD32" "#B0C4DE" "#00008A" "#8B795E"
[15] "#FDAE6B" "#66C2A5" "#276419" "#CD8C95" "#6A51A3" "#EEAD0E" "#0000FF"
[22] "#9ACD32" "#CD6090" "#CD5B45" "#8E0152" "#808000" "#67000D" "#3F007D"
[29] "#6BAED6" "#FC9272"
> getOldcol()
[1] "#E41A1C" "#377EB8" "#4DAF4A" "#984EA3" "#FF7F00" "#FFFF33" "#A65628"
[8] "#F781BF" "#999999" "#333333" "#A021EF" "#008A45" "#00008A"
>
>
>
>
>
> dev.off()
null device
1
>