Making an UpSet Plot

David S. Butcher

2020-06-30

UpSet plots

A data frame can be passed to to the make_UpSet_plot() argument as suggested in the “Loading and visualizing data” section.

Alternatively, make an UpSet plot by supplying a list of named lists. See the documentation for the UpSetR::upset() function for more information.

list <-
   list(
      list(
         "Fraction1" = c("A", "B", "C", "D", "E"),
         "Fraction2" = c("C", "D", "E", "F", "G")
      )
   )


viztools::make_UpSet_plot(list)

You can also supply any data frame with column names corresponding to fraction/replicate designations:

df <-
   data.frame(
      "Frac1" = c("A", "B", "C", "D", "E"),
      "Frac2" = c("C", "D", "E", "F", "G"),
      stringsAsFactors = FALSE
   )

viztools::make_UpSet_plot(df)

Here is an example showing real protein identifications from analysis of pre-fractionated E. coli MG1655 whole cell lysate. Data are taken from the PEPPI-MS manuscript supplementary results:

Arguments

The argument plotType can be used to change the X- and Y-axis labels. For example:

df <-
   data.frame(
      "Basket1" = c("Russet", "Yukon Gold", "Sweet", "Red", "Kennebec"),
      "Basket2" = c("Sweet", "Red", "Kennebec", "Yam", "La Ratte"),
      stringsAsFactors = FALSE
   )

viztools::make_UpSet_plot(
   df,
   plotType = "Potato"
)