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BoxPlot

Creates box plots for numeric data. There is one item for each sample group in a numeric matrix. Labels for items (on x axis) are retrieved from sample group table, or if it's not present, the numeric matrix. Label for the y axis can be customized. If there are NA values, the default is to ignore missing values in either the response or the group.

This is a simple example output.

LaTeX label for the section is 'sec:INSTANCE' and the figures are labeled as 'fig:INSTANCE_N'. INSTANCE is the name of the component instance and N refers to the number of the figure.

Version 1.3.1
Bundle tools
Categories Plot Quality Control Latex
Authors Kristian Ovaska (kristian.ovaska@helsinki.fi), Marko Laakso (Marko.Laakso@Helsinki.FI)
Issue tracker View/Report issues
Requires R ; sm (R-package)
Source files component.xml BoxPlot.r
Usage Example with default values

Inputs

Name Type Mandatory Description
in1 Matrix Mandatory Matrix data 1.
in2 Matrix Optional Matrix data 2.
in3 Matrix Optional Matrix data 3.
groups SampleGroupTable Optional If present, sample names are retrieved from here.
dataPoints CSV Optional If present, specified data points values to be drawn on top of the boxplot. This feature could be used for visual comparison of the values of the selected data points against the rest of the numeric data. For each data point its values for all the samples are present on the corresponding row in a matrix. The table references data points rows from the matrix in its first column. The second column, if present, defines labels of the data points to be drawn on the plot.

Outputs

Name Type Description
out Latex Latex subsection containing the box plots.

Parameters

Name Type Default Description
caption1 string "" Caption for plot 1 in the TeX section.
caption2 string "" Caption for plot 2 in the TeX section.
caption3 string "" Caption for plot 3 in the TeX section.
dpcm float 60 Dots per centimeter. Used for png-images.
drawLegend boolean false If TRUE, the legend with colors and labels for datapoints of interest is drawn. Otherwise, labels of the datapoints are drown on the top of the boxplots in over the corresponded lines.
height float 11 Height of each plot in cm.
outline boolean false Draw outliers as dots outside of the actual box plot, which is compressed respectively
pagebreak boolean false Tells if the result document should start with a page break.
plotPar string "" String to be evaluated in par() function. for example "bty='n', pch=7"
plotType string "boxplot" Choices are: boxplot, violin.
pngImage boolean false Switch image format between png and pdf
title1 string "" Main title for plot 1, e.g. "Log Ratio".
title2 string "" Main title for plot 2, e.g. "Log Ratio".
title3 string "" Main title for plot 3, e.g. "Log Ratio".
violinLineWidth float 1 Value for the violin plot line widths.
violinWidth float 1.2 Multiplier for the violin plot widths.
width float 14 Width of each plot in cm.
xvertical boolean true X axis labels are printed in vertical direction.
yHigh float -0.000001 High bound of the Y axis for all plots. If yLow and yHigh are the same, the values are computed from the data.
yLow float -0.000001 Low bound of the Y axis for all plots. If yLow and yHigh are the same, the values are computed from the data.
ylabel1 string "" Label for y axis in plot 1.
ylabel2 string "" Label for y axis in plot 2.
ylabel3 string "" Label for y axis in plot 3.

Test cases

Test case Parameters IN
in1
IN
in2
IN
in3
IN
groups
IN
dataPoints
OUT
out
case1 (missing) in1 in2 (missing) (missing) (missing) out
case2 properties in1 in2 (missing) (missing) (missing) out

title1=Title1,
title2=Title2,
outline=true

case3_numericnames (missing) in1 (missing) (missing) (missing) (missing) out
case4_violin properties in1 in2 (missing) (missing) (missing) out

title1=Title1,
title2=Title2,
plotType=violin,
yLow=-8,
yHigh=8

case5_png properties in1 in2 (missing) (missing) (missing) out

title1=Title1,
title2=Title2,
plotType=violin,
pngImage=true,
dpcm=40,
violinLineWidth=4,
yLow=-5,
yHigh=5,
caption1=Test caption 1.,
caption2=Test caption 2.

case6_yLimits properties in1 (missing) (missing) (missing) (missing) out

title1=Title1,
yLow=-5,
yHigh=5

case7_datapoints properties in1 in2 (missing) (missing) dataPoints out

title1=Title1,
title2=Title2,
outline=true

case8_datapoints_vio properties in1 in2 (missing) (missing) dataPoints out

title1=Title1,
title2=Title2,
plotType=violin,
yLow=-8,
yHigh=8,
drawLegend=true


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