Plot multiple genes from dds data

Question

[Fatemeh]

Hi everyone, I am struggling to find a way to plot the list of genes of my interest in a single pdf file using plotCounts(dds, gene = geneID) function. It just work perfectly when I want a single gene. As soon as I try to plot a list, it does not work. I even tried to use Style="Facet but it did not work. I would appreciate if someone can help me with this issue.

genes <- read.csv("./genes.csv", header=T)
geneID<-genes$igenename    
p<-plotCounts(dds, gene = geneID, intgroup = c("RANKL", "Genotype", "Background"),returnData=TRUE)

ggplot(p, aes(x = Genotype, y = count, color = Background, shape=RANKL)) + 
    geom_point(size=4, position=position_jitter(w = 0.1,h = 0)) +
        theme_bw() +
           theme(plot.title = element_text(hjust = 0.5))

Answer 1

[rpolicastro]

The function description states it's only for a single gene, so you need to loop through your gene IDs.

library("DESeq2")

dds <- makeExampleDESeqDataSet()
dds$time <- sample(1:3, ncol(dds), replace=TRUE)

gene_set <- c("gene1", "gene3", "gene10")
names(gene_set) <- gene_set

df <- lapply(gene_set, \(x) {
    y <- plotCounts(dds, x, c("condition", "time"), returnData=TRUE)
    y$feature <- x
    return(y)
})

df <- do.call(rbind, df)

This will give you a properly formatted long data.frame you can use in ggplot2.

[Fatemeh]

Thanks very much for your help. I tried this wonderful code and made the long data.frame but I do not know how I can plot this kind of data frame. I am sorry for this stupid question. Should it be also looped?

[rpolicastro]

You'll need to learn ggplot2 to really get the most out of it since it can make almost any plot type you want. Here's an example.

ggplot(df, aes(x=condition, y=count, color=as.factor(time))) +
  geom_jitter(
    position=position_jitterdodge(dodge.width=0.75),
    size=0.75) +
  geom_boxplot(
    position=position_dodge(width=0.5),
    fill=NA, width=0.25, outlier.shape=NA) +
  facet_grid(feature~.)

[Fatemeh]

Thank you very much for your big help. The problem with facet-grid is that it adds on all the graphs with the same scale. I have some genes which are lowly expressed and this way I do not see the differences clearly. If we could have for every single graph its own scale that would be awesome. I am not sure though if this is possible. Thanks one more time.