Question: SEURAT scRNA-seq and library contribution for each cluster
0
gravatar for Morris_Chair
4 days ago by
Morris_Chair170
Morris_Chair170 wrote:

Hello Everyone, I'm analyzing three replicates samples with Seurat pipeline and I made clusters in UMAP. I wanted to ask you if it's possible to know what is the contribution of each samples in terms of percentage for each cluster, I know R is capable of everything but I don't know how to code it,

could somebody help me with that?

Thank you in advance

-M

rna-seq • 115 views
ADD COMMENTlink modified 3 days ago by amjass20 • written 4 days ago by Morris_Chair170
2
gravatar for jared.andrews07
4 days ago by
jared.andrews074.2k
St. Louis, MO
jared.andrews074.2k wrote:

I prefer dittoSeq for tasks like this. It works on Seurat objects directly and has much better visualizations than Seurat. Should be included in the next Bioconductor release.

With dittoSeq, this would be done with:

dittoBarPlot("your_cluster_column", your_seurat_object, group.by = "your_sample_column")
ADD COMMENTlink written 4 days ago by jared.andrews074.2k

Thank you Jared.andrew for the answer, I was not able to install the package that includes dittoBarPlot case requires an upgrade version of R, but I solved the problem anyway

ADD REPLYlink written 3 days ago by Morris_Chair170
2
gravatar for amjass
3 days ago by
amjass20
amjass20 wrote:

you could also create a table breakdown of individual samples and then calculate total % per cluster: Would look like:

breakdown<-table(seuratObject@metadata$seurat_clusters, seuratObject@metadata$samples)

your output is a breakdown of all clusters and how many cells come from each sample in each one of those clusters. hope this helps!

ADD COMMENTlink written 3 days ago by amjass20
1

Hi Amjass, thank you very much for the code it worked perfectly fine, awesome !! :)

ADD REPLYlink written 3 days ago by Morris_Chair170

great! glad it helped :) enjoy!

ADD REPLYlink written 3 days ago by amjass20
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: 1119 users visited in the last hour