Question: Pull number of cells in cluster from seurat object
1
gravatar for cook.675
12 months ago by
cook.67540
cook.67540 wrote:

I've been working through some of the vignettes on the Satija Lab site. Specifically the control vs. treated data set found here:

https://satijalab.org/seurat/v3.1/immune_alignment.html

I don't know how to pull the number of cells in any given cluster, and I'm sure where this data is stored? To use the vignette example, the last line to compute the clusters is

immune.combined <- FindClusters(immune.combined, resolution = 0.5)

so it must be stored in immune.combined somewhere? How is it accssed?

Thanks!

seurat rna-seq • 2.8k views
ADD COMMENTlink modified 12 months ago • written 12 months ago by cook.67540

Thank this has been really helpful things are starting to come into focus.

How would I sub-out and create a table showing the number of cells per cluster by stimulation type?

I tried some of the following:

table(Immune.combined@meta.data$stim.seurat_clusters) table(immune.combined@meta.data$stim$seurat_clusters)

neither worked obviously

Or even if I could get the data individually and put them in a table my self.

I want to ask "How many cells in each cluster are from vehicle and how many are from the treatment group?

ADD REPLYlink modified 12 months ago • written 12 months ago by cook.67540

Please use ADD COMMENT/ADD REPLY when responding to existing posts to keep threads logically organized.

ADD REPLYlink written 12 months ago by genomax90k
1
gravatar for Haci
12 months ago by
Haci370
Haci370 wrote:

The cluster information is stored in the @meta.data slot and in a column something like res.0.5 as you used a resolution of 0.5 in your FindClusters() call. If you re-run FindClusters() with another resolution parameter, an additional column will be added.

To get the numbers in each cluster you can do something like table(seurat_object@meta.data$cluster_column).

The above is true for Seurat v2 but I would be surprised if these would be changed in v3.

ADD COMMENTlink written 12 months ago by Haci370
1
gravatar for Friederike
12 months ago by
Friederike6.2k
United States
Friederike6.2k wrote:

I usually assign the content of the metadata to a separate object, which tends to make subsequent manipulations easier.

I am a fan of the data.table package, but I'm sure there are solutions using the tidyverse/dplyr, too.

library(data.table)
library(magrittr)

## extract meta data
md <- immune.combined@meta.data %>% as.data.table
# the resulting md object has one "row" per cell

## count the number of cells per unique combinations of "Sample" and "seurat_clusters"
md[, .N, by = c("Sample", "seurat_clusters")]
    Sample seurat_clusters    N
 1:        KO               3  492
 2:        KO               1  786
 3:        KO               0 2031
 4:        KO               4  291
 5:        KO               7   95
 6:        KO               2  445
 7:        KO               5  140
 8:        KO               8   79
 9:        KO               9   50
10:       KO               6  130
11:         WT               1  996
12:         WT               0 3281
13:         WT               6  192
14:         WT               5  196
15:         WT               2  806
16:         WT               3  572
17:         WT               4  301
18:         WT               8   60
19:         WT               9   36
20:         WT               7   69

## with additional casting after the counting
md[, .N, by = c("Sample", "seurat_clusters")] %>% dcast(., Sample ~ seurat_clusters, value.var = "N")
   Sample    0   1   2   3   4   5   6  7  8  9
1:        KO  2031 786 445 492 291 140 130 95 79 50
2:         WT 3281 996 806 572 301 196 192 69 60 36
ADD COMMENTlink written 12 months ago by Friederike6.2k

Thanks so much for this I really appreciate it!

ADD REPLYlink written 12 months ago by cook.67540

Is there also a way to know which cell has gone into which cluster apart from just the number? is that data stored anywhere in Seurat?

ADD REPLYlink written 8 months ago by suvratha60

not sure I get what you mean. The cluster number specifies the cluster membership.

ADD REPLYlink written 5 months ago by Friederike6.2k

awesome and simple.

ADD REPLYlink written 5 months ago by jonathan.coquet0
0
gravatar for geek_y
12 months ago by
geek_y11k
Barcelona
geek_y11k wrote:

It will be stored in meta data. You can check by head(immune.combined@meta.data)

If you want to plot,

ggplot(immune.combined@meta.data, aes(V8, fill=V5))+geom_bar(stat="count")

V8 should be whatever column says seurat clusters. fill=V5 can be optional if you don't want to further sub classify the clusters

ADD COMMENTlink written 12 months ago by geek_y11k
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