1.3 Heat Map with Dendrogram

1 Summary
2 Tutorial
3 Heatmap with Dendrogram Dialog Box
4 HeatmapDendrogram X-Function (Pro)

Summary

The Heat Map with Dendrogram app can be used to

Impute missing values, standardize data and perform log2 transform
Perform hierarchical cluster analysis along columns and rows
Plot heat map with dendrogram

Tutorial

Right-click on the Heat Map with Dendrogram icon in the Apps Gallery and select Show in Folder.
The GSEData.ogw workbook file is in the pop-up folder. Open this workbook file in Origin.
Click on the Heat Map with Dendrogram icon to open the dialog.
In the dialog, select Rows from Standardize drop-down list. The dialog settings is shown as below.
Note: Pressing F1 key, the help file for this dialog will pop-up.
Click OK. A Heat Map graph is created. Double click on X axis, in the opened X Axis dialog, go to Tick Labels tab, select Format sub-tab, and choose 45 from Rotate (deg.) combo box. Click OK button.
The graph will look like as below.

Heatmap with Dendrogram Dialog Box

Input Data

Select data in the worksheet to plot heatmap with dendrogram.

Input Worksheet

Specify the worksheet for data to plot.

Column Labels in

Specify column labels for heatmap's x axis.

None

Use row number as heatmap's x axis tick labels.

1st Row

Use 1st row in the worksheet as heatmap's x axis tick labels.

Long Name

Use column's long Name in the worksheet as heatmap's x axis tick labels.

Units

Use column's Units in the worksheet as heatmap's x axis tick labels.

Comments

Use column's Comments in the worksheet as heatmap's x axis tick labels.

Row Labels in

Specify row labels for heatmap's y axis.

None

Use row number as heatmap's y axis tick labels.

1st Column

Use 1st column in the worksheet as heatmap's y axis tick labels.

Transform

Transform data before plotting.

Impute Missing Value

Specify the way to handle missing values.

None

Keep missing values

with Row Mean

Replace missing value with row mean.

with Column Mean

Replace missing value with column mean

Standardize

Specify the method to standardize variables.

None

Data are not standardized.

Columns

Columns are standardized with zero mean and unit standard deviation.

Rows

Rows are standardized with zero mean and unit standard deviation.

Log2 Transform

Specify whether to perform log2 transform.

Settings

Specify settings for the Hierarchical Cluster Analysis along columns and rows.

Cluster

Specify the dimension to cluster data.

Columns

Perform Hierarchical Cluster Analysis along rows and cluster columns.

Rows

Perform Hierarchical Cluster Analysis along columns and cluster rows.

Both

Perform Hierarchical Cluster Analysis along rows and cluster columns, then along columns and cluster rows.

Cluster Columns

Specify settings to cluster columns.

Cluster Method

Specify the linkage method to calculate the distance between a cluster and a new cluster. See cluster method options in Hierarchical Cluster Analysis

Distance Type

Specify a distance type to calculate the distance between two columns. See distance type options in Hierarchical Cluster Analysis

Number of Clusters

Specify the number of clusters. The value should be greater than 0 and no more than the number of columns.

Cluster Rows

Specify settings to cluster rows.

Cluster Method

Specify the linkage method to calculate the distance between a cluster and a new cluster. See cluster method options in Hierarchical Cluster Analysis

Distance Type

Specify a distance type to calculate the distance between two rows. See distance type options in Hierarchical Cluster Analysis

Number of Clusters

Specify the number of clusters. The value should be greater than 0 and no more than the number of rows.

Plot Data

Specify the worksheet for heatmap plot data.

Recalculate

Specify the way to recalculate and update the result if there is any change in the input data or settings.

None	The output will not be connected to the source data, and any change will not result in an update of the result. And you can't change settings to recalculate the result.
Auto	The result automatically updates when source data change. You can also change settings to recalculate the result.
Manual	The result will not automatically update when the source data changes. You must manually activate the update by clicking the Recalculate button in the Standard toolbar. You can also change settings to recalculate the result.

HeatmapDendrogram X-Function (Pro)

Brief Information

Perform hierarchical cluster analysis, and plot heatmap with dendrogram.

Command Line Usage

HeatMapDendrogram iw:=[Book1]Sheet1 -r 2 impute:=0 std:=2;

Variables

Display Name	Variable Name	I/O and Type	Default Value	Description
Input Worksheet	iw	Input Worksheet	<active>	Specify the worksheet for data to plot.
Column Labels in	clabel	Input int	2	Specify column labels for heatmap's x axis. Option list: 0:None Use row number as heatmap's x axis tick labels. 1:1st Row Use 1st row in the worksheet as heatmap's x axis tick labels. 2:Long Name Use column's long Name in the worksheet as heatmap's x axis tick labels. 3:Units Use column's Units in the worksheet as heatmap's x axis tick labels. 4:Comments Use column's Comments in the worksheet as heatmap's x axis tick labels.
Row Labels in	rlabel	Input int	1	Specify row labels for heatmap's y axis. Option list: 0:None Use row number as heatmap's y axis tick labels. 1:1st Column Use 1st column in the worksheet as heatmap's y axis tick labels.
Impute Missing Value	impute	Input int	0	Specify the way to handle missing values. Option list: 0:None Keep missing values 1:with Row Mean Replace missing value with row mean. 2:with Column Mean Replace missing value with column mean
Standardize	std	Input int	None	Specify the method to standardize variables. Option list: 0:None Data are not standardized. 1:Columns Columns are standardized with zero mean and unit standard deviation. 2:Rows Rows are standardized with zero mean and unit standard deviation.
Log2 Transform	log2	Input int	0	Specify whether to perform log2 transform.
Cluster	cluster	Input int	2	Specify the dimension to cluster data. Option list: 0:Columns Perform Hierarchical Cluster Analysis along rows and cluster columns. 1:Rows Perform Hierarchical Cluster Analysis along columns and cluster rows. 2:Both Perform Hierarchical Cluster Analysis along rows and cluster columns, then along columns and cluster rows.
Cluster Columns	trcol	Input TreeNode	<unassigned>	Specify settings to cluster columns.
Cluster Rows	trrow	Input TreeNode	<unassigned>	Specify settings to cluster rows.
Plot Data	od	Output Worksheet	[<new>]<new>!	Specify the worksheet for heatmap plot data.

trcol

The trcol treenode specifies settings to cluster columns.

Syntax: trcol.Treenode:= <value>

Example: trcol.nc:=2

Treenode	Label	Type	Default	Description
link	Cluster Method	int	2	Specify the linkage method to calculate the distance between a cluster and a new cluster. See cluster method options in hcluster X-Function.
dist	Distance Type	int	0	Specify a distance type to calculate the distance between two columns. See distance type options in hcluster X-Function.
nc	Number of Clusters	int	1	Specify the number of clusters. The value should be greater than 0 and no more than the number of columns.

trrow

The trrow treenode specifies settings to cluster rows.

Syntax: trrow.Treenode:= <value>

Example: trrow.nc:=2

Treenode	Label	Type	Default	Description
link	Cluster Method	int	2	Specify the linkage method to calculate the distance between a cluster and a new cluster. See cluster method options in hcluster X-Function.
dist	Distance Type	int	0	Specify a distance type to calculate the distance between two rows. See distance type options in hcluster X-Function.
nc	Number of Clusters	int	1	Specify the number of clusters. The value should be greater than 0 and no more than the number of rows.