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AttributeVisualizer

Visualizes multidimensional attributes using a heat map together with a clustering dendrogram. Each row in the heat map and each leaf in the clustering dendrogram corresponds to a data item such as a biological sample. The columns in the heat map are arbitrary attributes that may have numeric or category scale. Attribute values are visualized using coloring. Numeric attributes are colored using a color bar and category attributes using discrete colors. The dendrogram may be missing, in which case only attributes are visualized.

Example: the expression profiles of patiens have been measured using microarrays, providing an expression matrix. Also, clinical attributes such as age and gender are available for the patients. The component uses expression profiles for clustering the patients and visualizes clinical attributes using a heat map.

Example outputs: heat map, legend. See test case 1 for the corresponding input files.

Version 1.0.1
Bundle microarray
Categories Clustering Plot
Authors Kristian Ovaska (kristian.ovaska@helsinki.fi)
Issue tracker View/Report issues
Requires R ; cluster (R-package)
Source files component.xml AttributeVisualizer.r
Usage Example with default values

Inputs

Name Type Mandatory Description
annotation CSV Mandatory Annotation for the data items. One column (given by parameter idColumn) gives the data item ID that matches the column names in the matrix input. Other columns (given by parameter annotationColumns) contain annotations that are visualized in the heat map. Missing values are allowed, except not in the ID column.
matrix Matrix Optional Numeric matrix used for computing clusters. Each column is a vector that is associated to a data item (e.g. biological sample). Distance between data items i, j is defined as the Euclidean distance of the two vectors v_i, v_j. If missing, the clustering dendrogram is not shown.

Outputs

Name Type Description
report Latex Report that contains the heat map and a legend that describes the colors used in the heat map.

Parameters

Name Type Default Description
annotationColumns string "*" Columns in the annotation input that are visualized in the heat map. The special value * specifies all columns expect the ID column.
columnMargin float 7 Margin for column names in the image.
idColumn string "" Name of the data item ID column in the annotation input that matches column names in matrix. If empty, the first column is used.
rowMargin float 5 Margin for row names in the image.
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.
width float 16 Width of diagram in cm. Used for both heat map and the legend, although the legend only used full width if there are categorical attributes.

Test cases

Test case Parameters IN
annotation
IN
matrix
OUT
report
case1 (missing) annotation matrix report
case2 properties annotation matrix report

annotationColumns=Age,Treatment,
idColumn=Sample,
rowMargin=9

case3_nocluster properties annotation (missing) report

annotationColumns=Age,Treatment,
idColumn=Sample,
rowMargin=14,
columnMargin=8


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