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drawing Venn graph

Good morning everyone,

I am intend to draw a Venn graph. But I have a huge trouble to find the elements to draw it. In my dataset, there are two conditions of the samples. I want to check the different expression of gene markers in these two condition patients, but I failed to find the elements.

I hope you guys could give me some suggestions on how to find the same elements in my dataset.

Best

Andy

venn r
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written by Andy • Andy

Well, what did you try?

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written by swbarnes2 swbarnes2

I tried to use findallmarker() function, but I got an empty .csv file.

>fibroblast_class<-subset_data
 DefaultAssay(fibroblast_class)<-"RNA" 
 fibroblast_markers<-FindAllMarkers(fibroblast_class, only.pos = T, test.use = "MAST", min.pct = 0.25, logfc.threshold = 0.25, ident=c("organ")) #need to install MAST package 
write.csv(fibroblast_markers, "fibrb.markers_0.25_0.251116.csv") 
top10 <- fibroblast_markers %>% group_by(cluster) %>% top_n(n = 10, wt = avg_log2FC) 
fibroblast_class<-ScaleData(fibroblast_class) 
``

I also tried the way like we find the sub cluster, but I did not know why it says cannot find the idents, but I use table(data@active.ident) to check, and my ident is there.

• 0 views • link
written by Andy • Andy 
table(subset_data@active.ident)

pancreatic     kidney      liver       lung      skine 
      1017        461        137       1116       9583 

fibroblast_venn<-subset(subset_data, idents="organ")
Error in WhichCells.Seurat(object = x, cells = cells, idents = idents,  : 
  Cannot find the following identities in the object: organ
`

This is the code I used for find sub cluster.

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written by Andy • Andy

Well, you don't seem to have a category called "organ", so what exactly are you expecting that subset command to do?

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written by swbarnes2 swbarnes2

Since I am thinking my organ ident include pancreatic, kidney, liver, lung and skine, and I should set idents="organs".

I think you meant I should set idents="pancreatic"? like this to find the subset?

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written by Andy • Andy

I got your point!

I got the data finally!

😭

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written by Andy • Andy

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