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ClusterReport

Performs a hierarchical clustering of samples. The clustering is based on the given numeric row values of the numeric matrix and the results are shown on a LaTeX report fragment.

Version 1.1
Bundle tools
Categories Latex Clustering
Authors Kristian Ovaska (kristian.ovaska@helsinki.fi), Marko Laakso (Marko.Laakso@Helsinki.FI)
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Requires R ; cluster (R-package) ; igraph (R-package)
Source files component.xml ClusterReport.r
Usage Example with default values

Inputs

Name Type Mandatory Description
matr Matrix Mandatory Numeric data

Outputs

Name Type Description
report Latex Clustering report
tree GraphML Cluster dendrogram

Parameters

Name Type Default Description
cexSampleText float 1.0 A numerical value giving the amount by which the sample names in the plot tree should be scaled relative to the default values.
clusterMethod string "average" Name of clustering method. One of 'average', 'single' or 'complete'.
margin float 0 A numerical value giving the amount by which margin is increased.
rotateLabels boolean true If true, rotate column labels vertically in the distance matrix so that they take less space on the x axis.
sectionTitle string "Sample clusters" Title of the LaTeX section
sectionType string "subsection" Type of LaTeX section: usually one of section, subsection or subsubsection. If empty, no section statement is written.
showDistance boolean true This flag tells if the distance matrix shall be included into the document
width float 16 Width of diagram in cm

Test cases

Test case Parameters IN
matr
OUT
report
OUT
tree
case1 (missing) matr report tree
case2_twocolumns properties matr report tree

showDistance = false,
width = 10,
sectionTitle = Section title,
sectionType = section,
rotateLabels = false

case3_empty_input (missing) matr report tree

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