Hi, I have just run songbird and got the outputs,
I would like to plot the biplot in R but I am missing something to do with the colour? I have read that that can be due to the group being full of NAs (which it isn’t?)or being character, which it is.
regression_biplot <- read_qza('~/Documents/songbird_test/regression-biplot.qza') regression_biplot <- read_qza('~/Documents/songbird_test/regression-biplot.qza') regression_Eigvals<- regression_biplot$data$Eigvals regression_variance<- regression_biplot$data$ProportionExplained percentVar <- round(regression_variance*100) regression_biplot$data$Vectors %>% select(SampleID, PC1, PC2) %>% left_join(metadata) %>% ggplot(aes(x=PC1, y=PC2, color= `group`)) + geom_point(alpha=0.9) + theme_q2r() + scale_shape_manual(values=c(16,1), name="group") + scale_color_discrete(name="group")+ ggtitle("Regression biplot") + theme(plot.title = element_text(lineheight=.8, face="bold", size=12))
Error: Must request at least one colour from a hue palette.
My group column is a character (T or P)