Question: Sleuth PCA plots - how to change axis to percentage?
0
gravatar for BioBing
11 months ago by
BioBing90
Denmark
BioBing90 wrote:

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))
rna-seq kallisto pca sleuth R • 519 views
ADD COMMENTlink modified 4 weeks ago by bruce.moran410 • written 11 months ago by BioBing90
0
gravatar for bruce.moran
4 weeks ago by
bruce.moran410
Ireland
bruce.moran410 wrote:

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.

ADD COMMENTlink written 4 weeks ago by bruce.moran410
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1420 users visited in the last hour