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I have 2151 cells, I clustered them by Seurat to 5 clusters. With the code below, I am able to have the number of cells per cluster and per condition:

number_perCluster<- table(object@meta.data$conditions, 
                          object@meta.data$clusterID)

Could I please get a hint on how I could proceed to produce a figure where I say: X% of cells treated with condition "Y" are located in cluster "C" and so forth?

Thank you in advance.

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  • $\begingroup$ Have a look at prop.table, also if you want a figure, please describe it a bit more. This is usually better displayed as a table or heatmap, but perhaps you want something else... $\endgroup$ – llrs Feb 6 at 13:39
  • $\begingroup$ Please don't also create a github issue on the Seurat page each time you ask a question here, there is no need $\endgroup$ – TimStuart Feb 6 at 14:40
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Here is a solution using dplyr and ggplot2:

library(Seurat) 
library(dplyr)
library(ggplot2)

meta.data <- pbmc_small@meta.data

# create random classifications for the sake of this example
meta.data$condition <- sample(c('A', 'B', 'C'), nrow(meta.data), replace = TRUE)

counts <- group_by(meta.data, condition, res.1) %>% summarise(count = n())

ggplot(counts, aes(res.1, count, fill = condition)) +
  geom_bar(stat = 'identity')

enter image description here

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