Bioinformatics Toolbox™

get (clustergram) - Retrieve information about clustergram object

Syntax

get(CGobj) CGStruct = get(CGobj) PropertyValue = get(CGobj, 'PropertyName') [Property1Value, Property2Value, ...] = get(CGobj, 'Property1Name', 'Property2Name', ...)

Arguments

`CGobj`	Clustergram object created with the function `clustergram`.
`PropertyName`	Property name for a clustergram object.

Description

get(CGobj) displays all properties and their current values of CGobj, a clustergram object.

CGStruct = get(CGobj) returns all properties of CGobj, a clustergram object, to CGStruct, a scalar structure, in which each field name is a property of a clustergram object, and each field contains the value of that property.

PropertyValue = get(CGobj, 'PropertyName') returns the value of the specified property of CGobj, a clustergram object.

[Property1Value, Property2Value, ...] = get(CGobj, 'Property1Name', 'Property2Name', ...) returns the values of the specified properties of CGobj, a clustergram object.

Properties of a Clustergram Object

Property	Description
`RowLabels`	Vector of numbers or cell array of text strings to label the rows in the dendrogram and heat map. Default is a vector of values `1` through M, where M is the number of rows in `Data`, the matrix of data used by the `clustergram` function to create the clustergram object.
`ColumnLabels`	Vector of numbers or cell array of text strings to label the columns in the dendrogram and heat map. Default is a vector of values `1` through N, where N is the number of columns in `Data`, the matrix of data used by the `clustergram` function to create the clustergram object.
`RowGroupNames`	A cell array of text strings containing the names of the row groups exported to a clustergram object created using the Export Group to Workspace command in the Clustergram window.
`RowNodeNames`	A cell array of text strings containing the names of the row nodes exported to a clustergram object created using the Export Group to Workspace command in the Clustergram window.
`ColumnGroupNames`	A cell array of text strings containing the names of the column groups exported to a clustergram object created using the Export Group to Workspace command in the Clustergram window.
`ColumnNodeNames`	A cell array of text strings containing the names of the column nodes exported to a clustergram object created using the Export Group to Workspace command in the Clustergram window.
`ExprValues`	An M-by-N matrix of data, where M and N are the number of row nodes and column nodes respectively, exported to a clustergram object created using the Export Group to Workspace command in the Clustergram window. If the matrix contains gene expression data, typically each row corresponds to a gene and each column corresponds to a sample.
`Standardize`	Text string that specifies the dimension for standardizing the values in the data. The standardized values are transformed so that the mean is 0 and the standard deviation is 1 in the specified dimension. Possibilities are: `'Column (1)'` — Standardized along the columns of data. `'Row (2)'` — Standardized along the rows of data. `'None (3)'` — Did not perform standardization.
`Cluster`	Text string that specifies the dimension for clustering the values in the data. Possibilities are: `'Row (1)'` — Clustered rows of data only. `'Column (2)'` — Clustered columns of data only. `'All (3)'` — Clustered rows of data, then cluster columns of row-clustered data.
`RowPdist`	String or cell array that specifies the distance metric and optional arguments passed to the `pdist` function (Statistics Toolbox™ software) used to calculate the pairwise distances between rows. For information on possibilities, see the `pdist` function.
`ColumnPdist`	String or cell array that specifies the distance metric and optional arguments passed to the `pdist` function (Statistics Toolbox software) used to calculate the pairwise distances between columns. For information on possibilities, see the `pdist` function.
`Linkage`	String or two-element cell array of strings that specifies the linkage method passed to the `linkage` function (Statistics Toolbox software) used to create the hierarchical cluster tree for rows and columns. If a two-element cell array of strings, the first element is for linkage between rows, and the second element is for linkage between columns. For information on possibilities, see the `linkage` function.
`Dendrogram`	Scalar or two-element numeric vector or cell array that specifies the `'colorthreshold'` property passed to the `dendrogram` function (Statistics Toolbox software) used to create the dendrogram plot. If a two-element numeric vector or cell array, the first element is for the rows, and the second element is for the columns. For more information, see the `dendrogram` function.
`OptimalLeafOrder`	Property that enabled or disabled the optimal leaf ordering calculation, which determines the leaf order that maximizes the similarity between neighboring leaves. Possibilities are `1` (enabled) or `0` (disabled).
`LogTrans`	Controlled the log₂ transform of the data from natural scale. Possibilities are `1` (true) or `0` (false).
`ColorMap`	Either of the following: M-by-3 matrix of RGB values Name or function handle of a function that returns a colormap, such as `redgreencmap` or `redbluecmap`
`DisplayRange`	Positive scalar that specifies the display range of standardized values. For example, if you specify `redgreencmap` for the `'ColorMap'` property, pure red represents values ≥ `DisplayRange`, and pure green represents values ≤ –`DisplayRange`.
`SymmetricRange`	Property to force the color scale of the heat map to be symmetric around zero. Possibilities are `1` (true) or `0` (false).
`Ratio`	Either of the following: Scalar Two-element vector It specifies the ratio of space that the row and column dendrograms occupy relative to the heat map. If `Ratio` is a scalar, it is the ratio for both dendrograms. If `Ratio` is a two-element vector, the first element is for the ratio of the row dendrogram width to the heat map width, and the second element is for the ratio of the column dendrogram height to the heat map height. The second element is ignored for one-dimensional clustergrams.
`Impute`	Any of the following: Name of a function that imputes missing data. Handle to a function that imputes missing data. Cell array where the first element is the name of or handle to a function that imputes missing data and the remaining elements are property name/property value pairs used as inputs to the function.
`RowMarkers`	Optional structure array for annotating the groups (clusters) of rows determined by the `clustergram` function. Each structure in the array represents a group of rows and contains the following fields: `GroupNumber` — Number to annotate the row group. `Annotation` — String specifying text to annotate the row group. `Color` — String or three-element vector of RGB values specifying a color, which is used to label the row group. For more information on specifying colors, see `colorspec`. If this field is empty, default is `'blue'`.
`ColumnMarkers`	Optional structure array for annotating groups (clusters) of columns determined by the `clustergram` function. Each structure in the array represents a group of rows and contains the following fields: `GroupNumber` — Number to annotate the column group. `Annotation` — String specifying text to annotate the column group. `Color` — String or three-element vector of RGB values specifying a color, which is used to label the column group. For more information on specifying colors, see `colorspec`. If this field is empty, default is `'blue'`.

Examples

Load the MAT-file, provided with the Bioinformatics Toolbox™ software, that contains yeastvalues, a matrix of gene expression data.
```
load filteredyeastdata
```
Create a clustergram object and display the dendrograms and heat map from the gene expression data in the first 30 rows of the yeastvalues matrix.
```
cgo = clustergram(yeastvalues(1:30,:))
Clustergram object with 30 rows of nodes and 7 columns of nodes.
```

Use the get method to display the properties of the clustergram object, cgo.

get(cgo)

           RowLabels: {30x1 cell}
        ColumnLabels: {7x1 cell}
         Standardize: {'ROW (2)'}
             Cluster: {'ALL (3)'}
            RowPDist: {'Euclidean'}
         ColumnPDist: {'Euclidean'}
             Linkage: {'Average'}
          Dendrogram: {[0]}
    OptimalLeafOrder: 1
            LogTrans: 0
            Colormap: [11x3 double]
        DisplayRange: 3
      SymmetricRange: 1
               Ratio: [0.2000 0.2000]
              Impute: []
          RowMarkers: []
       ColumnMarkers: []

Export a clustergram object of a group (cluster) of rows to the MATLAB^® Workspace by right-clicking a node in the row dendrogram, and then selecting Export Group to Workspace.
In the Export to Workspace dialog box, type cgo2 for the Workspace variable name for the clustergram object, and then click OK.

Use the get method to display the properties of cgo2, the clustergram object of the exported group.

get(cgo2)

       RowGroupNames: {8x1 cell}
        RowNodeNames: {9x1 cell}
    ColumnGroupNames: {6x1 cell}
     ColumnNodeNames: {7x1 cell}
          ExprValues: [9x7 double]
         Standardize: {'ROW (2)'}
             Cluster: {'ALL (3)'}
            RowPDist: {'Euclidean'}
         ColumnPDist: {'Euclidean'}
             Linkage: {'Average'}
          Dendrogram: {[0]}
    OptimalLeafOrder: 1
            LogTrans: 0
            Colormap: [11x3 double]
        DisplayRange: 3
      SymmetricRange: 1
               Ratio: [0.2000 0.2000]
              Impute: []
          RowMarkers: []
       ColumnMarkers: []

get (clustergram) - Retrieve information about clustergram object

Syntax

Arguments

Description

Examples

See Also