How to plot combined bar graph in R

Question

[Bioinfo]

After running the following function

count_table <- table([e-mail]$seurat_clusters, [e-mail]$orig.ident, [e-mail]$singlr_labels)

View(count_table)

str(count_table)

 'table' int [1:15, 1:2, 1:20] 0 0 0 0 0 0 2 0 273 0 ...
 - attr(*, "dimnames")=List of 3
  ..$ : chr [1:15] "0" "1" "2" "3" ...
  ..$ : chr [1:2] "Sample1" "Sample2"
  ..$ : chr [1:20] "B_cell" "BM & Prog." "CMP" "DC" ...

I want to create a combined bar plot for that I used the following function but ends with an error.

ggplot(count_table) + geom_bar(aes(x=singlr_labels, fill=orig.ident), position = "dodge") + facet_wrap(~seurat_clusters)

Answer 1

[Nicolas Rosewick]

in R, table() is used to build contingency tables as specified in R doc : https://www.rdocumentation.org/packages/base/versions/3.6.2/topics/table

table uses the cross-classifying factors to build a contingency table of the counts at each combination of factor levels.

To build an actual table, or in the correct nomenclature a "dataframe" use data.frame() function Also rename the variable accordingly

count_table <- data.frame(seurat_clusters = [e-mail]$seurat_clusters, 
                               orig.ident = [e-mail]$orig.ident, 
                            singlr_labels = [e-mail]$singlr_labels)

Then plot

ggplot(count_table) + 
  geom_bar(aes(x=singlr_labels, fill=orig.ident), position = "dodge") + 
  facet_wrap(~seurat_clusters)

But you could directly use seurat metadata and plot it without building a temporary dataframe as :

[e-mail] %>%
  ggplot() +
  geom_bar(aes(x=singlr_labels, fill=orig.ident), position = "dodge") + 
  facet_wrap(~seurat_clusters)

Advice : Try to take a R basic course to familiarize with R syntax. Once that learned you will be much more confortable working using R.