Component: Plot2D

Plot2D

Creates scatter, line or bar plots where Y and X coordinates come from CSV files. Coordinates for the Y axis must always be provided; values for the X axis are optional. If X coordinates are missing, integers 1 to N are used. Multiple plots may be created simulateneously: each plot takes Y and X coordinates from one column in the input files "y" and "x". Columns are selected using parameters "yColumns" and "xColumns".

Each column may be plot to the same image or to different images. Creates also a pairs plot, which is each Y column ploted against all other Y columns. The X columns are discarded when using the pairs plot.

Version	1.0
Bundle	tools
Categories	Latex Plot
Authors	Kristian Ovaska (kristian.ovaska@helsinki.fi), Marko Laakso (Marko.Laakso@Helsinki.FI), Sirkku Karinen (sirkku.karinen@helsinki.fi)
Issue tracker	View/Report issues
Requires	R
Source files	component.xml Plot2D.r
Usage	Example with default values Plot2D( y = CSV, //x = CSV, //labels = CSV, //plotAnnotator = RSource, caption = "Scatter plot (%s)", colorFunction = "", commonScale = true, dpCm = 60, drawX = true, height = 11, imageType = "multiple", labelColumn = "", legendPosition = "off", nInf = -2e100, pInf = 2e100, plotPar = "", plotType = "p", pngImage = true, sectionTitle = "Two dimensional plot", sectionType = "subsection", sort = false, title = "%s", width = 14, xColumns = "", xHigh = -0.000001, xLabel = "x", xLow = -0.000001, xTransformation = "", yColumns = "", yHigh = -0.000001, yLabel = "y", yLow = -0.000001, yTransformation = "" )

Version

1.0

Bundle

tools

Categories

Latex Plot

Authors

Kristian Ovaska (kristian.ovaska@helsinki.fi), Marko Laakso (Marko.Laakso@Helsinki.FI), Sirkku Karinen (sirkku.karinen@helsinki.fi)

Issue tracker

View/Report issues

Requires

Source files

component.xml Plot2D.r

Usage

Example with default values

Inputs

Name	Type	Mandatory	Description
y	CSV	Mandatory	Coordinates on the Y axis. Columns from this file are selected for plotting using "yColumns".
x	CSV	Optional	Coordinates on the X axis. Columns from this file are selected for plotting using "xColumns". There must as many rows in "x" as there are in "y".
labels	CSV	Optional	Labels for the ploted columns. This file needs to have exactly the same number of labels as there are X and Y columns. Same labels will be assigned the same color.
plotAnnotator	RSource	Optional	R source file that is executed after the plot command. This can be used to add further elements to the plot. The current y and x values are available as numeric vectors "y.column" and "x.column". Current column names in y and x are available as strings "y.name" and "x.name". For example, "abline(h=max(y.column, na.rm=TRUE))" draws a horizontal line that intersects with the maximum Y coordinate.

Name

Type

Mandatory

Description

CSV

Mandatory

Coordinates on the Y axis. Columns from this file are selected for plotting using "yColumns".

CSV

Optional

Coordinates on the X axis. Columns from this file are selected for plotting using "xColumns". There must as many rows in "x" as there are in "y".

labels

CSV

Optional

Labels for the ploted columns. This file needs to have exactly the same number of labels as there are X and Y columns. Same labels will be assigned the same color.

plotAnnotator

RSource

Optional

R source file that is executed after the plot command. This can be used to add further elements to the plot. The current y and x values are available as numeric vectors "y.column" and "x.column". Current column names in y and x are available as strings "y.name" and "x.name". For example, "abline(h=max(y.column, na.rm=TRUE))" draws a horizontal line that intersects with the maximum Y coordinate.

Name	Type	Description
out	Latex	The plots. The type depends on the plotType parameter.

Name

Type

Description

out

Latex

The plots. The type depends on the plotType parameter.

Parameters

Name	Type	Default	Description
caption	string	"Scatter plot (%s)"	LaTeX caption of each figure. The caption may contain one or two %s placeholders, which are replaced with the current column names in "y" and "x" (if defined). Column names are not used when multiple plots are created to the same image (imageType = 'single').
colorFunction	string	""	Custom function for colors. Example c('red', 'blue', 'green') or rainbow(3) or rainbow(%d), in which %d is replaced with the number of different labels or columns in the plot. Default colors start from black and continue by rainbow()-function until each label or column is assigned with own color.
commonScale	boolean	true	If true, all plots have the same limits for X and Y axes. This makes it easier to compare plots. Only relevant when multiple columns have been selected.
dpCm	float	60	Dots per centimeter. Used for png-images.
drawX	boolean	true	If false, do not print X axis ticks and numbers.
height	float	11	Height of each plot in cm.
imageType	string	"multiple"	Plot multiple images = 'multiple', single image = 'single' or a pairs plot = 'pairs'
labelColumn	string	""	Columns in input "label" that is used. If not defined, uses the first column.
legendPosition	string	"off"	Legend position 'bottomleft' or 'topright' etc (Can not be used with the pairs plot)
nInf	float	-2e100	Substitution value for infinitely small values
pInf	float	2e100	Substitution value for infinitely great values
plotPar	string	""	String to be evaluated in par() function. for example "bty='n', pch=7"
plotType	string	"p"	Plot type p=points, l=lines, h=bars, bar=barplot
pngImage	boolean	true	Switch image format between png and pdf
sectionTitle	string	"Two dimensional plot"	Title of the LaTeX section or an empty string to omit the section
sectionType	string	"subsection"	Type of LaTeX section: usually one of section, subsection or subsubsection. No section statement is written if sectionTitle is empty.
sort	boolean	false	If true, sort values before plotting. This creates a cumulative-like distribution plot. (Can not be used with pairs plot)
title	string	"%s"	Image title. The caption may contain one or two %s placeholders, which are replaced with the current column names in "y" and "x" (if defined). Column names are not used when multiple plots are created to the same image (imageType = 'single').
width	float	14	Width of each plot in cm.
xColumns	string	"*"	Columns in input "x" that are plotted. The special value * includes all columns except non-numeric ones. There must be as many selected columns in X as there are in Y. Note that the files "y" and "x" may still contain a different number of columns.
xHigh	float	-0.000001	High bound of the X axis. The special value -0.000001 means that the bound is computed from the data.
xLabel	string	"x"	X axis label. The label may contain one %s placeholder, which is replaced with the current column name in "x", or if not defined, in "y".
xLow	float	-0.000001	Low bound of the X axis. The special value -0.000001 means that the bound is computed from the data.
xTransformation	string	""	Numeric R expression that is used to transform X values. The X values are available as a numeric matrix (or vector) under the name "x". This is analogous to "yTransformation".
yColumns	string	"*"	Columns in input "y" that are plotted. The special value * includes all columns except non-numeric ones.
yHigh	float	-0.000001	High bound of the Y axis. The special value -0.000001 means that the bound is computed from the data.
yLabel	string	"y"	X axis label. The label may contain one %s placeholder, which is replaced with the current column name in "y".
yLow	float	-0.000001	Low bound of the Y axis. The special value -0.000001 means that the bound is computed from the data.
yTransformation	string	""	Numeric R expression that is used to transform Y values. The Y values are available as a numeric matrix (or vector) under the name "y". Only those columns are present that are selected using "yColumns". For example, "-log10(y)" transforms Y values using a negative base 10 logarithm (defined only for positive values). The expression may be any legal R expression that takes a numeric matrix (or vector) and produces a matrix (or vector) of the same size.

Name

Type

Default

Description

caption

string

"Scatter plot (%s)"

LaTeX caption of each figure. The caption may contain one or two %s placeholders, which are replaced with the current column names in "y" and "x" (if defined). Column names are not used when multiple plots are created to the same image (imageType = 'single').

colorFunction

string

Custom function for colors. Example c('red', 'blue', 'green') or rainbow(3) or rainbow(%d), in which %d is replaced with the number of different labels or columns in the plot. Default colors start from black and continue by rainbow()-function until each label or column is assigned with own color.

commonScale

boolean

true

If true, all plots have the same limits for X and Y axes. This makes it easier to compare plots. Only relevant when multiple columns have been selected.

dpCm

float

Dots per centimeter. Used for png-images.

drawX

boolean

true

If false, do not print X axis ticks and numbers.

height

float

Height of each plot in cm.

imageType

string

"multiple"

Plot multiple images = 'multiple', single image = 'single' or a pairs plot = 'pairs'

labelColumn

string

Columns in input "label" that is used. If not defined, uses the first column.

legendPosition

string

"off"

Legend position 'bottomleft' or 'topright' etc (Can not be used with the pairs plot)

nInf

float

-2e100

Substitution value for infinitely small values

pInf

float

2e100

Substitution value for infinitely great values

plotPar

string

String to be evaluated in par() function. for example "bty='n', pch=7"

plotType

string

"p"

Plot type p=points, l=lines, h=bars, bar=barplot

pngImage

boolean

true

Switch image format between png and pdf

sectionTitle

string

"Two dimensional plot"

Title of the LaTeX section or an empty string to omit the section

sectionType

string

"subsection"

Type of LaTeX section: usually one of section, subsection or subsubsection. No section statement is written if sectionTitle is empty.

sort

boolean

false

If true, sort values before plotting. This creates a cumulative-like distribution plot. (Can not be used with pairs plot)

title

string

"%s"

Image title. The caption may contain one or two %s placeholders, which are replaced with the current column names in "y" and "x" (if defined). Column names are not used when multiple plots are created to the same image (imageType = 'single').

width

float

Width of each plot in cm.

xColumns

string

"*"

Columns in input "x" that are plotted. The special value * includes all columns except non-numeric ones. There must be as many selected columns in X as there are in Y. Note that the files "y" and "x" may still contain a different number of columns.

xHigh

float

-0.000001

High bound of the X axis. The special value -0.000001 means that the bound is computed from the data.

xLabel

string

"x"

X axis label. The label may contain one %s placeholder, which is replaced with the current column name in "x", or if not defined, in "y".

xLow

float

-0.000001

Low bound of the X axis. The special value -0.000001 means that the bound is computed from the data.

xTransformation

string

Numeric R expression that is used to transform X values. The X values are available as a numeric matrix (or vector) under the name "x". This is analogous to "yTransformation".

yColumns

string

"*"

Columns in input "y" that are plotted. The special value * includes all columns except non-numeric ones.

yHigh

float

-0.000001

High bound of the Y axis. The special value -0.000001 means that the bound is computed from the data.

yLabel

string

"y"

X axis label. The label may contain one %s placeholder, which is replaced with the current column name in "y".

yLow

float

-0.000001

Low bound of the Y axis. The special value -0.000001 means that the bound is computed from the data.

yTransformation

string

Numeric R expression that is used to transform Y values. The Y values are available as a numeric matrix (or vector) under the name "y". Only those columns are present that are selected using "yColumns". For example, "-log10(y)" transforms Y values using a negative base 10 logarithm (defined only for positive values). The expression may be any legal R expression that takes a numeric matrix (or vector) and produces a matrix (or vector) of the same size.

Test cases

Test case	Parameters▼	IN y	IN x	IN labels	IN plotAnnotator	OUT out
case1	properties	y	(missing)	(missing)	(missing)	out
	xLabel=X (%s), yLabel=Y (%s), pInf =9, nInf =1
case10_clusters	properties	y	x	labels	(missing)	out
	imageType=single, drawX=false, sort=true, legendPosition=topleft, labelColumn=Cluster, colorFunction=rainbow(%d), dpCm=40, title=Clusters
case11_barplot	properties	y	(missing)	(missing)	(missing)	out
	xLabel=X (%s), yLabel=Y (%s), plotType=bar, legendPosition=topright, commonScale=true, yLow=0
case12_barplot_single	properties	y	x	(missing)	(missing)	out
	xLabel=X (%s), yLabel=Y (%s), plotType=bar, imageType=single, legendPosition=topright, yLow=0, xColumns=C1,C1, yColumns=C2,C3
case2_x	properties	y	x	(missing)	(missing)	out
	xColumns=X2,X3
case3_transformation	properties	y	x	(missing)	(missing)	out
	xColumns=X2,X3, yTransformation=log2(y), xTransformation=x+10
case4_annotator	properties	y	x	(missing)	plotAnnotator	out
	xColumns=X2,X3, commonScale=false
case5_bounds	properties	y	x	(missing)	(missing)	out
	xColumns=X2,X3, xLow=0, yLow=-5, yHigh=8, commonScale=false
case6_annotator_column	properties	y	x	(missing)	(missing)	out
	yColumns=Y1, xColumns=X2, xTransformation=-log10(x), yTransformation=-log10(y)
case7_empty_input	(missing)	y	(missing)	(missing)	(missing)	out
case8_pairs	properties	y	(missing)	(missing)	(missing)	out
	imageType=pairs, title=Pairs
case9_lines	properties	y	(missing)	(missing)	(missing)	out
	imageType=single, plotType=l, drawX=false, sort=true, legendPosition=topleft, colorFunction=rainbow(%d), title=Expressions

Test case

Parameters▼

IN
y

IN
x

IN
labels

IN
plotAnnotator

OUT
out

case1

properties

(missing)

out

xLabel=X (%s),
yLabel=Y (%s),
pInf =9,
nInf =1

case10_clusters

properties

labels

(missing)

out

imageType=single,
drawX=false,
sort=true,
legendPosition=topleft,
labelColumn=Cluster,
colorFunction=rainbow(%d),
dpCm=40,
title=Clusters

case11_barplot

properties

(missing)

out

xLabel=X (%s),
yLabel=Y (%s),
plotType=bar,
legendPosition=topright,
commonScale=true,
yLow=0

case12_barplot_single

properties

(missing)

out

xLabel=X (%s),
yLabel=Y (%s),
plotType=bar,
imageType=single,
legendPosition=topright,
yLow=0,
xColumns=C1,C1,
yColumns=C2,C3

case2_x

properties

(missing)

out

xColumns=X2,X3

case3_transformation

properties

(missing)

out

xColumns=X2,X3,
yTransformation=log2(y),
xTransformation=x+10

case4_annotator

properties

(missing)

plotAnnotator

out

xColumns=X2,X3,
commonScale=false

case5_bounds

properties

(missing)

out

xColumns=X2,X3,
xLow=0,
yLow=-5,
yHigh=8,
commonScale=false

case6_annotator_column

properties

(missing)

out

yColumns=Y1,
xColumns=X2,
xTransformation=-log10(x),
yTransformation=-log10(y)

case7_empty_input

(missing)

(missing)

out

case8_pairs

properties

(missing)

out

imageType=pairs,
title=Pairs

case9_lines

properties

(missing)

out

imageType=single,
plotType=l,
drawX=false,
sort=true,
legendPosition=topleft,
colorFunction=rainbow(%d),
title=Expressions

Anduril

Plot2D

Inputs

Outputs

Parameters

Test cases