question ablout seurat figure PC_contribution

Question

[yueli7]

Hello,

Anyone now what is the mean of following figure?

I know it is the PC_1, what is the number in x-axis?

It comes from single-cell RNA-seq Seurat package.

Thanks in advance for any help!

Best,

Yue

Answer 1

[Kevin Blighe]

It alludes to the importance of each gene in relation to PC1. If, for example, PC1 accounts for 70% variation in your dataset, then these genes are the main sources of that variation. Sign / directionality is important: for example, it implies that MALAT1 will be higher in certain samples whose loading values are negative along PC1, whereas the reverse is true for all other genes in this plot that you are showing.

It is essentially plotting the same as that produced by my own function, plotLoadings(), from PCAtools: Determine the variables that drive variation among each PC

Kevin

[yueli7]

Hello, Kevin Blighe,

Thank you so much for your response!

Thank you so much for your useful linkage.

I really appreciated!

Thank you again!

Best,

Yue