[R] Problem with creating a PCA graph in a loop

[gavin duley]

Hi all,

I am having enormous problems with a loop that iterates over different
levels in the factor wine.data$Time (levels T06, T09, and T12) and
creates a PCA and graph for individuals at that time only. These
graphs need to be accessible outside the loop, so I can combine them
using ggpubr::ggarrange to produce a figure for a paper.

The difficulty I am having is with the labels produced by
ggrepel::geom_label_repel. Since the loop uses the variable i to set
the level of wine.data$Time, when used outside the loop the labels
produced by geom_label_repel are always for T12 (i.e., the last level
run by the loop).

Oddly, this only affects the labels: the title, set using
ggtitle(paste0("PCA of wine.data observations at Time ", print(i))),
shows the correct time, and the datapoints are for the correct time.

Is there some way to get geom_label_repel to read current_rownames and
store the values in the ggplot object, rather than to reload them
every time I display or save the ggplot graph?

Thanks!
gavin,

Code for reference. I can provide a sample dataset for reproducibility
if needed.

for(i in levels(wine.data$Time)){
  print(i)
  wine.data.filt <- filter(wine.data,Time == i)
  current_rownames <- rownames(wine.data.filt)
  wine.data.filt.pca <- dudi.pca(wine.data.filt[3:11],
                               nf=6,
                               scannf=F)
  wine.data_quanti_sup <- wine.data.filt[,12, drop = FALSE]
  head(wine.data_quanti_sup)

  # Colour by Treatment
  assign(paste0("individ_", i),
         fviz_pca_ind(wine.data.filt.pca,
                      geom.ind = "point",
                      mean.point=F,
                      col.ind = wine.data.filt$Treatment,
                      ellipse.type = "confidence",
                      legend.title = "Groups"
         )+ggtitle(paste0("PCA of wine.data observations at Time ", print(i)))
         +
           scale_colour_manual(
             values = c(
               "Control" = "#00A087FF",
               "Low" = "#3C5488FF",
               "High" = "#E64B35FF")
           ) + geom_label_repel(position =
ggpp::position_nudge_center(0.2, 0.1, 0, 0),
                                box.padding = 0.5,
                                max.overlaps = Inf,
                                aes(label=current_rownames,
                                    colour=wine.data.filt$Treatment
                                )
           ) +
           scale_fill_manual(
             values = c(
               "Control" = "#00A087FF",
               "Low" = "#3C5488FF",
               "High" = "#E64B35FF")
           ))
}