7.6 UpSet Plots

An UpSet plot is an alternative to a Venn diagram. It is not limited to visualizing differential analysis results, though I have found this to be a common use case. Another is to compare the protein identifications between groups of samples.

# Filter to significant features
temp <- filter(t_res2, adj.P.Val < 0.05)
# List of significant features by contrast
input_list <- split(temp$RefSeq, temp$contrast)
# UpSet plot
plot_upset(input_list)

216 proteins are only significant in the “Proliferative-Immunoreactive” comparison, 191 are only significant in the “Mesenchymal-Immunoreactive” comparison, 35 are significant in both the “Differentiated-Immunoreactive” and “Proliferative-Immunoreactive” comparisons, etc.