cellHTS2 HTML report settings

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Description

Functions to control the output of writeReport through session-wide or call-specific settings.

Usage

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Arguments

x

A named list of settings. See details for supported values.

Details

The 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 setSettings function by providing a named nested list of values. The latter can be set by passing a similiar list on to writeHTML as the optional settings argument. The current values for all available settings can be queried using the 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:

plateList

The settings for all the plots in the plate list section of the report. There are several sub-section:

correlation

The settings for the correlation plots:

size

The width in inches of the pdf device holding the plot. The default value is 7.5.

fontSize

The point size of the font for all the text in the pdf version of the plot. The default value is 14.

font

The font used for all the text in the pdf version of the plot. The default is "Helvetica".

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.

thumbFontSize

The point size of the font for all the text in the thumbnail png version of the plot. The default value is 12.

maplot

The settings for the correlation plots:

size

The width in inches of the pdf device holding the plot. The default value is 7.5.

fontSize

The point size of the font for all the text in the pdf version of the plot. The default value is 14.

font

The font used for all the text in the pdf version of the plot. The default is "Helvetica".

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.

thumbFontSize

The point size of the font for all the text in the thumbnail png version of the plot. The default value is 12.

histograms

The settings for the histogram plots:

size

The width in inches of the pdf device holding the plot. The default value is 8.

fontSize

The point size of the font for all the text in the pdf version of the plot. The default value is 14.

font

The font used for all the text in the pdf version of the plot. The default is "Helvetica".

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.

thumbFontSize

The point size of the font for all the text in the thumbnail png version of the plot. The default value is 10.

type

The type of plot produced here. One in histogram or 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.

reproducibility

The settings for the reproducibility plate plots:

size

The width in inches of the pdf device holding the plot. The default value is 8.

fontSize

The point size of the font for all the text in the pdf version of the plot. The default value is 12.

font

The font used for all the text in the pdf version of the plot. The default is "Helvetica".

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.

thumbFontSize

The point size of the font for all the text in the thumbnail png version of the plot. The default value is 10.

col

The color range that gets passed on to plotPlate as argument col. The default value is brewer.pal(9, "YlOrRd").

range

The data range that gets passed on to plotPlate as argument xrange. The default value is function(x) c(0, quantile(x, 0.95, na.rm=TRUE)).

include

A logical indicating whether to create the plate plot or not. The default value is FALSE.

map

A logical indicating whether to tooltips containing the plate annotation for each well or not. The default value is FALSE.

average

The settings for the reproducibility plate plots:

size

The width in inches of the pdf device holding the plot. The default value is 8.

fontSize

The point size of the font for all the text in the pdf version of the plot. The default value is 12.

font

The font used for all the text in the pdf version of the plot. The default is "Helvetica".

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.

thumbFontSize

The point size of the font for all the text in the thumbnail png version of the plot. The default value is 10.

col

The color range that gets passed on to plotPlate as argument col. The default value is brewer.pal(9, "YlOrRd").

range

The data range that gets passed on to plotPlate as argument xrange. The default value is function(x) c(0, quantile(x, 0.95, na.rm=TRUE)).

include

A logical indicating whether to create the plate plot or not. The default value is FALSE.

map

A logical indicating whether to tooltips containing the plate annotation for each well or not. The default value is FALSE.

intensities

The settings for the raw data plate plots:

size

The width in inches of the pdf device holding the plot. The default value is 8.

fontSize

The point size of the font for all the text in the pdf version of the plot. The default value is 12.

font

The font used for all the text in the pdf version of the plot. The default is "Helvetica".

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.

thumbFontSize

The point size of the font for all the text in the thumbnail png version of the plot. The default value is 10.

col

The color range that gets passed on to plotPlate as argument col. The default value is rev(brewer.pal(9, "RdBu")).

range

The data range that gets passed on to plotPlate as argument xrange. The default value is function(x) quantile(x, c(0.025, 0.975), na.rm = TRUE). A useful alternative setting here would be function(x) c(-1,1) * max(abs(x), na.rm=TRUE), which forces a value of 0 to be white.

include

A logical indicating whether to create the plate plot or not. The default value is FALSE.

map

A logical indicating whether to tooltips containing the plate annotation for each well or not. The default value is FALSE.

plateConfiguration

This controls settings for the plate configuration part of the report. Available settings are:

size

The width in inches of the pdf device holding the plot. The default value is 14.

fontSize

The point size of the font for all the text in the pdf version of the plot. The default value is 12.

font

The font used for all the text in the pdf version of the plot. The default is "Helvetica".

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.

thumbFontSize

The point size of the font for all the text in the thumbnail png version of the plot. The default value is 9.

include

A logical indicating whether to create the plate configuration plot or not. The default value is TRUE.

plateSummaries

This controls settings for the plate summary plots in the report. There are two sub-sections:

boxplot
size

The width in inches of the pdf device holding the plot. The default value is 7.5.

fontSize

The point size of the font for all the text in the pdf version of the plot. The default value is 12.

font

The font used for all the text in the pdf version of the plot. The default is "Helvetica".

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.

thumbFontSize

The point size of the font for all the text in the thumbnail png version of the plot. The default value is 11.

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 c("pink", "lightblue").

controls
size

The width in inches of the pdf device holding the plot. The default value is 7.5.

fontSize

The point size of the font for all the text in the pdf version of the plot. The default value is 12.

font

The font used for all the text in the pdf version of the plot. The default is "Helvetica".

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.

thumbFontSize

The point size of the font for all the text in the thumbnail png version of the plot. The default value is 11.

screenSummary

The settings for all the plots in the screen summary section of the report. There are several sub-section:

scores

The settings for summary screen image plots:

size

The width in inches of the pdf device holding the plot. The default value is 7.

fontSize

The point size of the font for all the text in the pdf version of the plot. The default value is 10.

font

The font used for all the text in the pdf version of the plot. The default is "Helvetica".

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.

thumbFontSize

The point size of the font for all the text in the thumbnail png version of the plot. The default value is 9.

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 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 list(posNeg=rev(brewer.pal(11, "RdBu"))[c(1:5, rep(6,3), 7:11)], pos=brewer.pal(9, "Greys")).

aspect

The aspect ratio of the plot. The default value is 1.

annotation

An alternative character vector of annotation mappings. See imageScreen for details.

map

A logical indicating whether to tooltips containing the plate annotation for each well or not. The default value is FALSE.

range

The range of values into which the colors will be mapped. A numeric of length 2.

nbImageBins

The number of color bins used in the map. Default is 256.

nbLegendBins

The number of color bins shown in the legend. Default is 7.

qqplot

The settings for the Normal Q-Q plots:

size

The width in inches of the pdf device holding the plot. The default value is 7.

fontSize

The point size of the font for all the text in the pdf version of the plot. The default value is 10.

font

The font used for all the text in the pdf version of the plot. The default is "Helvetica".

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.

thumbFontSize

The point size of the font for all the text in the thumbnail png version of the plot. The default value is 9.

distribution

The settings for the density distribution plot:

size

The width in inches of the pdf device holding the plot. The default value is 7.

fontSize

The point size of the font for all the text in the pdf version of the plot. The default value is 10.

font

The font used for all the text in the pdf version of the plot. The default is "Helvetica".

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.

thumbFontSize

The point size of the font for all the text in the thumbnail png version of the plot. The default value is 9.

screenResults

The settings for the screen results panel:

keepFieldPattern

A regular expression indicating which column names to keep. Default is "^plate$|^well$|^score$|^wellAnno$|^finalWellAnno$|raw_|normalized_|GeneID|GeneSymbol".

htmlMaxItems

The maximal number of cells in the output table to produce an HTML table. Default is 20000.

htmlLinks

A data frame containing a plate column, a well column, followed by the columns containing the HTML hyper links to add to the output table. Default is NULL, no links.

controls

The settings for the annotation of control wells and other type of wells. Currently these are only two item:

col

A named vector of colors to be used across all plots for the annotation of the well types. Allowed values are: sample, neg, controls, other, empty, flagged, act, inh and 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 otherCol.

col

A color palette from which colors are drawn for well types not defined in col.

controls

Global report settings:

ppi

A numeric indicating the resolution of the screen. This parameter is used to generate PNG images. Large numbers produce large PNG images. Default is 72.

Value

The current settings for getSettings.

setSettings is called for its side effect of setting session-wide settings.

Author(s)

Florian Hahne

See Also

writeReport

Examples

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oset <- getSettings()
oset

setSettings(list(plateConfiguration=list(size=2),
list(plateList=list(intensities=list(include=FALSE)))))

getSettings()

setSettings(oset)

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