Hi all, I have an error when plotting a PCA graph on R studio. My graph seems to come back where the height dimension is very small making a thin rectangular graph compared to a square. I believe it is due to the scaling on the y and x axis being the same yet PC1 represents 96% variance compared to PC2% representing 2%. Is there a way to change the scaling size within DESeq2:plotPCA without using other programs? I have tried exporting or copying the graph but it still has this issue.

Thanks!

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Plot PCA is a pretty bare bones simple little plotter, and you can't change much with it. To get more control, you are going to have to make the plot yourself, then you can control its dimensions, and stretch that Y axis like you want. I can tell you that with ggplot2, you can add coord_fixed(ratio = 1.5) to fix the proportions. I don't know how to do it with plot or plotly, so you'll have to google that.