Center or fix a sample at 0 on PC1 in PCA plot
1
0
Entering edit mode
3.3 years ago

We have recently noticed a group that is consistently able to publish PCA plots with their sample of interest seemingly aligned at 0 on PC1 or both PC1 and PC2 . In their methods they only mention that they use the R prcomp() function. We are interested to understand how they might be doing this. Attached is an example plot showing sample X at 0 on both the PC1 and PC2 axis.

Example PCA plot

Bulk RNA-Seq PCA • 1.1k views
ADD COMMENT
2
Entering edit mode
3.3 years ago

My guess is that they're just picking their reference sample, determining the offsets for PC1/2 to get it to 0, and then applying that same offset to all of the other samples prior to plotting as well.

ADD COMMENT
0
Entering edit mode

Another approach is to calculate the distance of each point to your reference (PC1), set PC1 to 0 and use the distance to position the other points.

ADD REPLY

Login before adding your answer.

Traffic: 1346 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6