Question: question ablout seurat figure PC_contribution
0
gravatar for yueli7
5 days ago by
yueli750
China
yueli750 wrote:

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

figure1

enter image description here

rna-seq • 85 views
ADD COMMENTlink modified 5 days ago by Kevin Blighe51k • written 5 days ago by yueli750
1
gravatar for Kevin Blighe
5 days ago by
Kevin Blighe51k
Kevin Blighe51k wrote:

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

ADD COMMENTlink modified 5 days ago • written 5 days ago by Kevin Blighe51k
1

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

ADD REPLYlink written 5 days ago by yueli750
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1290 users visited in the last hour