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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
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Categories Latex Plot
Authors Kristian Ovaska (kristian.ovaska@helsinki.fi), Marko Laakso (Marko.Laakso@Helsinki.FI), Sirkku Karinen (sirkku.karinen@helsinki.fi)
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Requires R
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.

Outputs

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.

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


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