Plot a well statistic in false color representation or
using a self-defined grid plotting function. The
plot is supposed to resemble the physical geometry of a microtitre
plate.
Numeric vector of length ncol*nrow or matrix with
ncol*nrow rows (except if argument ind is specified).
If of class matrix, the use of argument gridFun is expected.
nrow
Numeric of length 1. The number of rows of the plate.
ncol
Numeric of length 1. The number of columns of the plate.
col
Character vector. Usually the names of two or three colors
between which the color map is interpolated, using the function
colorRampPalette.
ind
Optional integer vector of equal length as x. It
indicates the position of the respective value of
x on the plate. Can be used to adress the problem of missing
values. Each well that is not allocated a value of x by
ind will not be plotted.
xrange
Numeric vector of length two giving thwe range of
x that is mapped into the color scale. Alternatively, this
can be a function which takes the values of x as input and
creates such a vector.
na.action
Character. One of "zero""omit" or
"xout".
How should the wells for which x is NA be treated?
For "zero", they are plotted as if the value were 0.
For "omit", they are omitted.
For "xout", they are crossed out.
When x is a matrix, na.action is only applied to rows
containing nothing but NAs. Further special treatment of NA
values in matrices need to be implemented in gridFun.
main
Character of length 1. Plot title.
char
An optional character vector of equal length as x
(except if argument ind is specified) to be used for well
annotation. Each element of the
vector may contain a string to be superimposed on
the respective well or NA for no plotting.
desc
Character of length 2. Legend for the two extremes of the
colorbar, e.g. 'act' and 'inh'.
add
Logical. If TRUE add plate plot to current plot. May
be used when plotting in grid layout panels.
gridFun
Character. The name of the plotting function to create
individual graphs for each well. See functions .drawCircle
and .drawPie
for examples.
funArgs
Dataframe with argument values to be passed to
gridCall. For each argument specified in gridCall there must be one column
with the argument name as colname and the argument values for every
well.
...
Further graphical parameters that can be used to control
the output of plotPlate.
cex.main:
expansion factor for title.
cex.lab:
expansion factor for label.
cex.char:
expansion factor for well annotation.
cex.legend:
expansion factor for well legend labels.
cex.desc:
expansion factor for well legend description.
Details
You may use this function either to create plots showing a
single-value per well statistic for microtiter plates, or you can use a
self-made plotting function using a combination of any valid grid
commands to produce arbitrary plots in a plate array format. These plots
may also show multifactorial data. Self-defined plotting functions need
to have data as first argument. plotPlate passes all data
values for the respective well to the plotting function. Any further
arguments may be passed on using argument funArgs. See
.drawCircle and .drawPie for examples of valid plotting
functions and the vignette for detailed information. Note that
using funCall overrides some of the default functionalities,
e.g. plotting of legends and alters the treatment of NA values.
Argument ind allows the user to indicate the position (well
number) for each element of vector x on the plate. This can be
used either to change the order in which elements of x are to be
plotted or to deal with the problem of missing data for some of the
wells on a plate.
To further increase the amount of information of the platePlot one may
decorate wells with short annotations using argument char. Each
element of char!= NA will be superimposed on the respective
well (see examples).
Value
The function produces a plot in the active graphics device.
It returns a list withfour elements. The element which is a vector with
the indices of those elements in x that were plotted (see argument
na.action). The element coord is a length(which) by 4
matrix in which each row specifies the corners of a rectangle that contains a
well. It is intended to be used as an argument to a subsequent call to
imageMap. Elements width and
height may be used to open a graphic devices that can hold the plate
plot with the correct aspect ratio.
R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> library(prada)
Loading required package: Biobase
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
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
Loading required package: RColorBrewer
Loading required package: grid
Loading required package: rrcov
Loading required package: robustbase
Attaching package: 'robustbase'
The following object is masked from 'package:Biobase':
rowMedians
Scalable Robust Estimators with High Breakdown Point (version 1.3-11)
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/prada/plotPlate.Rd_%03d_medium.png", width=480, height=480)
> ### Name: plotPlate
> ### Title: Plot a well statistic for microtiter plates.
> ### Aliases: plotPlate
> ### Keywords: hplot
>
> ### ** Examples
>
> plotPlate(runif(96), main="example 1", col=c("#0000e0", "#e00000"), desc=c("act", "inh"))
> plotPlate(runif(384), nrow=16, ncol=24, main="example 2", col=c("#0000e0", "white", "#e00000"))
> plotPlate(runif(48), main="example 3", col=c("#0000e0", "#e00000"), ind=c(1:24, 73:96))
> x <- runif(96)
> x[sample(96, 10)] <- NA
> plotPlate(x, main="example 4", col=c("#0000e0", "#e00000"),
+ char=c(rep(NA, 72), LETTERS[1:24]), na.action="xout")
> plotPlate(runif(96, min=0.1, max=0.5), gridFun=".drawCircle")
> plotPlate(matrix(runif(288), ncol=3), gridFun=".drawPie",
+ funArgs=as.data.frame(matrix(2:4, ncol=3, nrow=96, byrow=TRUE)))
>
>
>
>
>
>
> dev.off()
null device
1
>