ggplot and DESeq2 PCA plot

Question

[biology_inform]

Hi all, I am trying to convert my PCA plot which is created with DESeq2 to ggplot object but somehow I couldnt manage to do it.

pcaPlot <- plotPCA(dds, intgroup = "types", ntop = nrow(dds), returnData = TRUE) 
annotated_pcaPlot <- ggplot(geom_text(pcaPlot,aes(label=name,group=group)))+geom_text(size = 3,position = position_nudge(y = -0.03))+
  theme_test(base_family = "Arial") +geom_point(aes(color=group))+scale_color_manual(values=c('Purple3','Orangered'))

Error in validate_mapping(): ! mapping must be created by aes() Run rlang::last_error() to see where the error occurred. rlang::last_error() <error/rlang_error> Error in validate_mapping(): ! mapping must be created by aes() --- Backtrace:

1. ggplot2::ggplot(geom_text(pcaPlot, aes(label = name, group = group)))
2. ggplot2::geom_text(pcaPlot, aes(label = name, group = group))
3. ggplot2::layer(...)
4. ggplot2:::validate_mapping(mapping) Run rlang::last_trace() to see the full context.

I am getting this error when I run like above. Do you have any recommendations ?

[Basti]

I believe there is an inadequate geom_text after introducing ggplot() that should not be here

Answer 1

[Trivas]

Your issue is with the following:

ggplot(geom_text(pcaPlot,aes(label=name,group=group)))

You should instead do:

ggplot(pcaPlot, aes(label = name, group = group))+
    geom_text()+