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Sleuth PCA plots - how to change axis to percentage?

Hi all,

I was wondering if there is an easy way in "plot_pca" of the Sleuth package (R package for analyzing Kallisto output) to add percentages on x and y labels?

Thanks!

Cheers, Birgitte

plot_pca(so, pc_x=1L, pc_y = 2L, use_filtered = TRUE,
    units = "tpm", text_labels=FALSE, color_by = "treat",
    point_size = 7, point_alpha = 0.8) +
  theme(axis.text.y=element_text(size=10),
        axis.text.x = element_text(size=10),
        legend.position = "bottom",
        legend.text = element_text(size=10),
        legend.title = element_blank()) +
  scale_x_continuous(limits = c(-9000,9000)) + 
  scale_y_continuous(limits = c(-8000,8000))
r sleuth rna-seq kallisto pca
• 4,116 views • link
updated by bruce.moran bruce.moran • written by BioBing BioBing

1 answer

I had the same question, so for anyone else coming across this:

ppv <- plot_pc_variance(so)
PCpc <- ppv$data$var
names(PCpc) <- paste0("PC", seq(1:length(PCpc)))

Also NB from here that TPM is probably not a good input to PCA.

• 1 views • link
written by bruce.moran bruce.moran

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