I'd like to generate a PCA of my bulk RNAseq data, coloured by each of my variables in the DESeq2 object "vsd". My current code looks like this (to generate a single plot):
pcaData <- plotPCA(vsd, intgroup=c("Age", "BlastRate"), returnData=TRUE)
percentVar <- round(100 * attr(pcaData, "percentVar"))
ggplot(pcaData, aes(PC1, PC2, color=Age, shape=BlastRate)) +
geom_point(size=3) +
xlab(paste0("PC1: ",percentVar[1],"% variance")) +
ylab(paste0("PC2: ",percentVar[2],"% variance")) +
geom_text(aes(label=name),hjust=-.2, vjust=0) +
ggtitle("Principal Component Analysis")
Can anyone suggest a method to loop through and swap "Age" with the other variable columns of vsd?
>head(colData(vsd),1)
DataFrame with 1 row and 14 columns
LibSize LibDiversity PercMapped Age SpermStatus SpConc SpMot Subject.Group PairedSample FertRate
<factor> <factor> <factor> <factor> <character> <factor> <factor> <factor> <factor> <factor>
sRNA_1 Low High High 42-46 unk unk unk Male-Male 2 Low
BlastRate RNABatch LibPrepBatch sizeFactor
<factor> <factor> <factor> <numeric>
sRNA_1 Low 1 6 0.929408
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If I understand correctly, you might try :
pcaData <- plotPCA(vsd, intgroup=c("Age", "BlastRate"), returnData=TRUE)
percentVar <- round(100 * attr(pcaData, "percentVar"))
for (k in colnames(pcaData)){
ggplot(pcaData, aes_string("PC1", "PC2", color=k, shape=BlastRate)) +
geom_point(size=3) +
xlab(paste0("PC1: ",percentVar[1],"% variance")) +
ylab(paste0("PC2: ",percentVar[2],"% variance")) +
geom_text(aes(label=name),hjust=-.2, vjust=0) +
ggtitle("Principal Component Analysis")
}
You may change colnames(pcaData) to a list of variable you want to test.
I tried your suggestion and got this error. I'm not sure why I get this error when running your loop but not when I run my code as above. Notably I'm working in Rstudio so each one of these code blocks is a chunk.
Error in aes_string("PC1", "PC2", color = k, shape = BlastRate) :
object 'BlastRate' not found
Note that intgroup in the first line needs to contain every element of colData that you might want to include. So you may as put them all in; there's no reason not to.
Also note the difference between aes() and aes_string(), how one takes barewords, and one takes quoted strings.
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