\name{settings}
\alias{settings}
\alias{getSettings}
\alias{setSettings}
\title{
cellHTS2 HTML report settings
}
\description{
Functions to control the output of \code{\link{writeReport}} through
session-wide or call-specific settings.
}
\usage{
setSettings(x)
getSettings()
}
\arguments{
\item{x}{A named list of settings. See details for supported values.}
}
\details{
The \code{\link{writeReport}} function produces a complete audit
trail of the analysis in the form of an HTML report. The content of
this report is highly customizable though session-wide and also
though call-specific settings. The former are supposed to be set using
the \code{setSettings} function by providing a named nested list of
values. The latter can be set by passing a similiar list on to
\code{writeHTML} as the optional \code{settings} argument. The
current values for all available settings can be queried using the
\code{getSettings} function.
Similar to the structure of the HTML report, the available settings
are broken up into subsections, and the names of these subsection
have to be matched by the names in the nestes list structure:
\describe{
\item{plateList}{The settings for all the plots in the plate list
section of the report. There are several sub-section:
\describe{
\item{correlation}{The settings for the correlation plots:
\describe{
\item{size}{The width in inches of the pdf device holding the
plot. The default value is 7.5.}
\item{fontSize}{The point size of the font for all the text in the
pdf version of the plot. The default value is 14.}
\item{font}{The font used for all the text in the pdf version
of the plot. The default is \code{"Helvetica"}.}
\item{thumbFactor}{The factor by which the thumbnail png
version of the plot is smaller compared to the
high-resolution pdf version. The default value is 1.5.}
\item{thumbFontSize}{The point size of the font for all the
text in the thumbnail png version of the plot. The default
value is 12.}
}
}
\item{maplot}{The settings for the correlation plots:
\describe{
\item{size}{The width in inches of the pdf device holding the
plot. The default value is 7.5.}
\item{fontSize}{The point size of the font for all the text in the
pdf version of the plot. The default value is 14.}
\item{font}{The font used for all the text in the pdf version
of the plot. The default is \code{"Helvetica"}.}
\item{thumbFactor}{The factor by which the thumbnail png
version of the plot is smaller compared to the
high-resolution pdf version. The default value is 1.5.}
\item{thumbFontSize}{The point size of the font for all the
text in the thumbnail png version of the plot. The default
value is 12.}
}
}
\item{histograms}{The settings for the histogram plots:
\describe{
\item{size}{The width in inches of the pdf device holding the
plot. The default value is 8.}
\item{fontSize}{The point size of the font for all the text in the
pdf version of the plot. The default value is 14.}
\item{font}{The font used for all the text in the pdf version
of the plot. The default is \code{"Helvetica"}.}
\item{thumbFactor}{The factor by which the thumbnail png
version of the plot is smaller compared to the
high-resolution pdf version. The default value is 2.}
\item{thumbFontSize}{The point size of the font for all the
text in the thumbnail png version of the plot. The default
value is 10.}
\item{type}{The type of plot produced here. One in
\emph{histogram} or \emph{density}. Both plot types have
pros and cons: histograms can be misleading because of
bin size artefacts, whereas density plots hide the sample
size information.}
}
}
\item{reproducibility}{The settings for the reproducibility
plate plots:
\describe{
\item{size}{The width in inches of the pdf device holding the
plot. The default value is 8.}
\item{fontSize}{The point size of the font for all the text in the
pdf version of the plot. The default value is 12.}
\item{font}{The font used for all the text in the pdf version
of the plot. The default is \code{"Helvetica"}.}
\item{thumbFactor}{The factor by which the thumbnail png
version of the plot is smaller compared to the
high-resolution pdf version. The default value is 1.3.}
\item{thumbFontSize}{The point size of the font for all the
text in the thumbnail png version of the plot. The default
value is 10.}
\item{col}{The color range that gets passed on to
\code{\link[prada]{plotPlate}} as argument
\code{col}. The default value is \code{brewer.pal(9,
"YlOrRd")}.}
\item{range}{The data range that gets passed on to
\code{plotPlate} as argument \code{xrange}. The default
value is \code{ function(x) c(0, quantile(x, 0.95,
na.rm=TRUE))}.}
\item{include}{A logical indicating whether to create the
plate plot or not. The default value is \code{FALSE}.}
\item{map}{A logical indicating whether to tooltips
containing the plate annotation for each well or not. The
default value is \code{FALSE}.}
}
}
\item{average}{The settings for the reproducibility
plate plots:
\describe{
\item{size}{The width in inches of the pdf device holding the
plot. The default value is 8.}
\item{fontSize}{The point size of the font for all the text in the
pdf version of the plot. The default value is 12.}
\item{font}{The font used for all the text in the pdf version
of the plot. The default is \code{"Helvetica"}.}
\item{thumbFactor}{The factor by which the thumbnail png
version of the plot is smaller compared to the
high-resolution pdf version. The default value is 1.3.}
\item{thumbFontSize}{The point size of the font for all the
text in the thumbnail png version of the plot. The default
value is 10.}
\item{col}{The color range that gets passed on to
\code{\link[prada]{plotPlate}} as argument
\code{col}. The default value is \code{brewer.pal(9,
"YlOrRd")}.}
\item{range}{The data range that gets passed on to
\code{plotPlate} as argument \code{xrange}. The default
value is \code{ function(x) c(0, quantile(x, 0.95,
na.rm=TRUE))}.}
\item{include}{A logical indicating whether to create the
plate plot or not. The default value is \code{FALSE}.}
\item{map}{A logical indicating whether to tooltips
containing the plate annotation for each well or not. The
default value is \code{FALSE}.}
}
}
\item{intensities}{The settings for the raw data
plate plots:
\describe{
\item{size}{The width in inches of the pdf device holding the
plot. The default value is 8.}
\item{fontSize}{The point size of the font for all the text in the
pdf version of the plot. The default value is 12.}
\item{font}{The font used for all the text in the pdf version
of the plot. The default is \code{"Helvetica"}.}
\item{thumbFactor}{The factor by which the thumbnail png
version of the plot is smaller compared to the
high-resolution pdf version. The default value is 1.6.}
\item{thumbFontSize}{The point size of the font for all the
text in the thumbnail png version of the plot. The default
value is 10.}
\item{col}{The color range that gets passed on to
\code{plotPlate} as argument \code{col}. The default
value is \code{rev(brewer.pal(9, "RdBu"))}.}
\item{range}{The data range that gets passed on to
\code{plotPlate} as argument \code{xrange}. The default
value is \code{function(x) quantile(x, c(0.025, 0.975),
na.rm = TRUE)}. A useful alternative setting here would
be \code{function(x) c(-1,1) * max(abs(x), na.rm=TRUE)},
which forces a value of \code{0} to be white.}
\item{include}{A logical indicating whether to create the
plate plot or not. The default value is \code{FALSE}.}
\item{map}{A logical indicating whether to tooltips
containing the plate annotation for each well or not. The
default value is \code{FALSE}.}
}
}
}
}
\item{plateConfiguration}{This controls settings for the plate
configuration part of the report. Available settings are:
\describe{
\item{size}{The width in inches of the pdf device holding the
plot. The default value is 14.}
\item{fontSize}{The point size of the font for all the text in the
pdf version of the plot. The default value is 12.}
\item{font}{The font used for all the text in the pdf version
of the plot. The default is \code{"Helvetica"}.}
\item{thumbFactor}{The factor by which the thumbnail png
version of the plot is smaller compared to the
high-resolution pdf version. The default value is 2.}
\item{thumbFontSize}{The point size of the font for all the
text in the thumbnail png version of the plot. The default
value is 9.}
\item{include}{A logical indicating whether to create the plate
configuration plot or not. The default value is \code{TRUE}.}
}
}
\item{plateSummaries}{This controls settings for the plate
summary plots in the report. There are two sub-sections:}
\describe{
\item{boxplot}{
\describe{
\item{size}{The width in inches of the pdf device holding the
plot. The default value is 7.5.}
\item{fontSize}{The point size of the font for all the text in the
pdf version of the plot. The default value is 12.}
\item{font}{The font used for all the text in the pdf version
of the plot. The default is \code{"Helvetica"}.}
\item{thumbFactor}{The factor by which the thumbnail png
version of the plot is smaller compared to the
high-resolution pdf version. The default value is 1.5.}
\item{thumbFontSize}{The point size of the font for all the
text in the thumbnail png version of the plot. The default
value is 11.}
\item{col}{The colors used to fill the boxes. A vector of
length two, where the first item specifies the color for
the raw data panel and the second item specifies the
color for the normalized data panel. The default value is
\code{c("pink", "lightblue")}.}
}
}
\item{controls}{
\describe{
\item{size}{The width in inches of the pdf device holding the
plot. The default value is 7.5.}
\item{fontSize}{The point size of the font for all the text in the
pdf version of the plot. The default value is 12.}
\item{font}{The font used for all the text in the pdf version
of the plot. The default is \code{"Helvetica"}.}
\item{thumbFactor}{The factor by which the thumbnail png
version of the plot is smaller compared to the
high-resolution pdf version. The default value is 1.5.}
\item{thumbFontSize}{The point size of the font for all the
text in the thumbnail png version of the plot. The default
value is 11.}
}
}
}
\item{screenSummary}{The settings for all the plots in the screen summary
section of the report. There are several sub-section:
\describe{
\item{scores}{The settings for summary screen image plots:
\describe{
\item{size}{The width in inches of the pdf device holding the
plot. The default value is 7.}
\item{fontSize}{The point size of the font for all the text in the
pdf version of the plot. The default value is 10.}
\item{font}{The font used for all the text in the pdf version
of the plot. The default is \code{"Helvetica"}.}
\item{thumbFactor}{The factor by which the thumbnail png
version of the plot is smaller compared to the
high-resolution pdf version. The default value is 1.}
\item{thumbFontSize}{The point size of the font for all the
text in the thumbnail png version of the plot. The default
value is 9.}
\item{col}{The color range used to map the data values
into. This has to be a named list of length two, with the
first item \code{posNeg} being the color range used when
there are both positive and negative values, and the
second item being the color range for positive values
only. One usually wants the former to be centered on
white to blend into the background, and the former to
start from white. The default value is
\code{list(posNeg=rev(brewer.pal(11, "RdBu"))[c(1:5,
rep(6,3), 7:11)], pos=brewer.pal(9, "Greys"))}.}
\item{aspect}{The aspect ratio of the plot. The default
value is \code{1}.}
\item{annotation}{An alternative character vector of
annotation mappings. See \code{\link{imageScreen}} for
details.}
\item{map}{A logical indicating whether to tooltips
containing the plate annotation for each well or not. The
default value is \code{FALSE}.}
\item{range}{The range of values into which the colors will
be mapped. A numeric of length 2.}
}
}
\item{qqplot}{The settings for the Normal Q-Q plots:
\describe{
\item{size}{The width in inches of the pdf device holding the
plot. The default value is 7.}
\item{fontSize}{The point size of the font for all the text in the
pdf version of the plot. The default value is 10.}
\item{font}{The font used for all the text in the pdf version
of the plot. The default is \code{"Helvetica"}.}
\item{thumbFactor}{The factor by which the thumbnail png
version of the plot is smaller compared to the
high-resolution pdf version. The default value is 1.}
\item{thumbFontSize}{The point size of the font for all the
text in the thumbnail png version of the plot. The default
value is 9.}
}
}
\item{distribution}{The settings for the density distribution
plot:
\describe{
\item{size}{The width in inches of the pdf device holding the
plot. The default value is 7.}
\item{fontSize}{The point size of the font for all the text in the
pdf version of the plot. The default value is 10.}
\item{font}{The font used for all the text in the pdf version
of the plot. The default is \code{"Helvetica"}.}
\item{thumbFactor}{The factor by which the thumbnail png
version of the plot is smaller compared to the
high-resolution pdf version. The default value is 1.}
\item{thumbFontSize}{The point size of the font for all the
text in the thumbnail png version of the plot. The default
value is 9.}
}
}
}
}
\item{controls}{The settings for the annotation of control wells
and other type of wells. Currently these are only two item:
\describe{
\item{col}{A named vector of colors to be used across all plots
for the annotation of the well types. Allowed values are:
\code{sample}, \code{neg}, \code{controls}, \code{other},
\code{empty}, \code{flagged}, \code{act}, \code{inh} and
\code{pos}. Additional user-defined well types that don't
fall in any of these groups will be assigned a color from the
palette defined in \code{otherCol}.}
\item{col}{A color palette from which colors are drawn for well
types not defined in \code{col}.}
}
}
}
}
\value{
The current settings for \code{getSettings}.
\code{setSettings} is called for its side effect of setting
session-wide settings.
}
\author{
Florian Hahne
}
\seealso{
\code{\link{writeReport}}
}
\examples{
oset <- getSettings()
oset
setSettings(list(plateConfiguration=list(size=2),
list(plateList=list(intensities=list(include=FALSE)))))
getSettings()
setSettings(oset)
}