PCA

This guide provides step-by-step instructions on how to perform Principal Component Analysis (PCA) on a VCF file. It explains how to upload the file, select parameters, customize the plot, and save the results. The guide also offers tips on color options and provides options for colorblind-friendly plots.

Alex Sandercock
13 steps
2 minutes

127.0.0.1

You can use any VCF file in this tab as long as it contains information in the GT FORMAT field. If you only have a file that does not contain this, but contains read counts, you can use the "Dosage Calling" tab to estimate dosage calls for the samples which will then populate the GT Format Field.\ \ All VCF files generated in BIGapp will have this information.

On the left hand menu, click "PCA".

Click "Browse..." to select the VCF file to upload.

Click "Browse..." to select passport file to upload.

Choose Passport file "browse" selection highlighted

Click the "Species Ploidy\*" field and type the species ploidy

Click "Run Analysis".

Click here to select the variable to color the PCA by.

Color Variable for PCA plot parameters selection highlighted

Click "2D-Plot" to view a standard 2-D PCA plot.

Plot Controls

Users can select various plot controls for the PCA plots including changing colors, the axis being viewed, etc. This can help users explore relationships between samples and groupings of samples.

Click on "Color Palette" to change the color palette of the plots.

Color Palette drop down menu highlighted

Colorblind friendly color options are also available to use.

Color palette color blind friendly options

Clicking on the "X-Axis" for 2D-Plots only can adjust the PC axis viewed in the plot.

Click here to choose specific items to color in the 2-D PCA plot.

Color specific category within variable toggle button highlighted

Click here to select the category of items to color. *Please note that multiple items can be selected to color.*

Select category to color drop down button highlighted

Click here to change the color of the unselected items in the 2-D PCA plot

Download a plot image

Click this button to download a plot image.

You have completed this training module for creating PCAs in the BIGapp. Return to the main training page to learn more about other BIGapp features.

PCA

Alex Sandercock
13 steps
2 minutes