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| SubtitleText | Principal components analysis plot in 3D. Each dot is a sample and samples originating from the same biological source (dependent study design) are connected by lines. The axes show the first three principal components, with the fraction of explained variance in the parenthesis |
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| AnchorName | pca-3d |
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If you want to change a color, select the Customize colors hyperlink. The resulting dialog (Figure 5) will enable you to replace an existing color by a color of your choice (click on the arrow head 
to invoke the color mixer) or add more colors (Add color)....
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| SubtitleText | Customize colors dialog (default appearance). General tab (palette) is used for sample coloring and general sample attribute-based coloring in the chromosome view, hierarchical clustering, and general charts and graphs. Two-color numeric tab (palette) is used to color by numeric sample attribute in the hierarchical clustering, principal components analysis, and dot plot views. Save button saves your color preferences |
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| AnchorName | custom-colors |
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When click on a dot (sample), it will be selected and a label of the sample will be displayed, from the Label by drop-down list to select how to label the selected sample. To select more than one samples, press ctrl Ctrl & click.
Next, Show legend turns the legend on or off. Select all selects all the dots, while Show axis turns the coordinate axis on or off. To change the size of the dots, use the Dot size slider. Grid cells increases or decreases the size of the cells in the plot grid and the Major grid interval specifies the frequency of major grid lines (fat lines). E.g. setting the Major grid interval to 4 highlights every 4th grid line.
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You can also reduce the number of dimensions of the plot by switching the Plot style to 2D (Figure 6 is based on the same data as Figure 2, but is plotted in 2D).
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Figure 6:
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| SubtitleText | Principal components analysis plot in 2D. Each dot is a sample. The axes show the first two principal components, with the fraction of explained variance in the parenthesis (an example) |
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| AnchorName | pca-2d |
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Although first three PCs are shown by default, you can plot any of the first nine PCs, by using the X, Y, and Z drop-down lists.
Once you are pleased with the appearance of the dot plot, push Save image button to save it to the local machine. The resulting dialog (Figure 7) controls the resolution of the image file. The image will be saved in png format, and the default filename is PCA plot.png. Or, if you are not happy with your edits, you can always revert to the initial view by pushing the Reset button.
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Figure 7:
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| SubtitleText | Save image dialog (default settings) |
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