DendrogramFormatting.pdf

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Contents

Dendrogram Formatting

Overview

The Dendrogram Formatting shows basic formatting methods on Dendrogram views from hierarchical clustering on an -Omic data object's observations and/or variables. Array Studio can easily handle Heatmap Rows/Columns sorting, Chart Properties, Color Properties, X/Y-Axis labels, Color Borders, and ColorBars etc.

To format Dendrogram view, go to View Controller | Task | Data/Properties/Customize.

Dendrogram control.png

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Data

Sort Heatmap Rows and Columns

This module works only after hiding X/Y-Axis Dendrograms (Thumbnails).

Hide thumbnails.png

After hiding the X-Axis Dendrogram, the heatmap columns could be sorted by options in the design table:

Sort heatmap columns.png

The same as sorting heatmap columns, after hiding Y-Axis Dendrogram, users could sort heatmap rows:

Sort heatmap rows.png

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Scales

By default the Dendrogram Heatmap is scaled by RobustCenterScale, users could change the scale by specify normalization: Heatmap Scales

Specify normalization.png

Properties

Chart Properties

In Chart Properties window, users could modify Text formatting, background color, title formatting, X/Y Axis formatting, labels, label rotations etc.

To hide labels on Y-Axis, check Y Axis in the Chart Propeties window, set the Show Scale to False:

Hide labels.png

To rotate labels on X-Axis, check X Axis in the Chart Propeties window, under Scale tab, input 90 to the Rotation option.

Rotate labels.png

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Color Properties

The color properties of the Dendrogram heatmap could be edited through Change Color Properties:

Color properties.png


Customize

Add border for labels on X/Y Axis

Users could add color bars for X or Y axis, to show the borders of each column or row. Click the "Change X-Axis ClorBars" under the Customize tab, move "group" and "treatment" to the right panel, click OK, the colorbar will show up in the dendrogram view.

XaxisColorbar.png

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sub group X/Y labels

The generated view could show multi labels for X/Y axis.

Sub group xlabels.png

As shown in the above screenshot, X axis labels are subgrouped by group -> treatment -> chip.

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OmicScript

Hierarchical Clustering

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Related Articles

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