setSettings: cellHTS2 HTML report settings
In cellHTS2: Analysis of cell-based screens - revised version of cellHTS
Description
Usage
Arguments
Details
Value
Author(s)
See Also
Examples
Description
Functions to control the output of writeReport through
session-wide or call-specific settings.
Usage
1
2
setSettings(x)
getSettings()
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
Examples
1
2
3
4
5
6
7
8
9
oset <- getSettings()
oset
setSettings(list(plateConfiguration=list(size=2),
list(plateList=list(intensities=list(include=FALSE)))))
getSettings()
setSettings(oset)
cellHTS2 documentation built on Nov. 8, 2020, 6 p.m.
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Description Usage Arguments Details Value Author(s) See Also Examples
Description
Functions to control the output of writeReport through
session-wide or call-specific settings.
Usage
1 2 | setSettings(x)
getSettings()
|
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
plotPlateas argumentcol. The default value isbrewer.pal(9, "YlOrRd").- range
The data range that gets passed on to
plotPlateas argumentxrange. The default value isfunction(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
plotPlateas argumentcol. The default value isbrewer.pal(9, "YlOrRd").- range
The data range that gets passed on to
plotPlateas argumentxrange. The default value isfunction(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
plotPlateas argumentcol. The default value isrev(brewer.pal(9, "RdBu")).- range
The data range that gets passed on to
plotPlateas argumentxrange. The default value isfunction(x) quantile(x, c(0.025, 0.975), na.rm = TRUE). A useful alternative setting here would befunction(x) c(-1,1) * max(abs(x), na.rm=TRUE), which forces a value of0to 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
posNegbeing 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 islist(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
imageScreenfor 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
platecolumn, awellcolumn, followed by the columns containing the HTML hyper links to add to the output table. Default isNULL, 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,inhandpos. Additional user-defined well types that don't fall in any of these groups will be assigned a color from the palette defined inotherCol.- 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
Examples
1 2 3 4 5 6 7 8 9 | oset <- getSettings()
oset
setSettings(list(plateConfiguration=list(size=2),
list(plateList=list(intensities=list(include=FALSE)))))
getSettings()
setSettings(oset)
|
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