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Component
AttributeVisualizerVisualizes 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 |
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|---|---|---|---|---|---|---|
| case1 | (missing) | annotation | matrix | report | ||
| case2 | properties | annotation | matrix | report | ||
|
annotationColumns=Age,Treatment, |
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| case3_nocluster | properties | annotation | (missing) | report | ||
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annotationColumns=Age,Treatment, |
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