Component: BoxPlot

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.

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 BoxPlot( in1 = Matrix, //in2 = Matrix, //in3 = Matrix, //groups = SampleGroupTable, //dataPoints = CSV, caption1 = "", caption2 = "", caption3 = "", dpcm = 60, drawLegend = false, height = 11, outline = false, pagebreak = false, plotPar = "", plotType = "boxplot", pngImage = false, title1 = "", title2 = "", title3 = "", violinLineWidth = 1, violinWidth = 1.2, width = 14, xvertical = true, yHigh = -0.000001, yLow = -0.000001, ylabel1 = "", ylabel2 = "", ylabel3 = "" )

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.

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.

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

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.

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

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

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

Value for the violin plot line widths.

violinWidth

float

1.2

Multiplier for the violin plot widths.

width

float

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

Test case

Parameters▼

IN
in1

IN
in2

IN
in3

IN
groups

IN
dataPoints

OUT
out

case1

(missing)

(missing)

case2

(missing)

title1=Title1,
title2=Title2,
outline=true

case3_numericnames

(missing)

(missing)

case4_violin

(missing)

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

case5_png

(missing)

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