IN-RICHES/upset_plot.R at main · lauramason326/IN-RICHES · GitHub

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library(tidyverse)
library(dplyr)
library(ComplexHeatmap)

data <- read.csv("~/Documents/Wrighton_lab/Agribiome/AG ML project/metadata_for_upset.csv", header = TRUE) %>%
  filter(seq =="FALSE")%>%
select(3:33)
names(data)

m <- make_comb_mat(data)

ncol(data)

UpSet(m,
      pt_size = unit(3, 'mm'),
      lwd = 1,
      set_order = c("program",
                   "research",
                   "Unknown",
                   "Cropping",
                   "Grazing",
                    "Alfalfa",
                    "Annual.Grasses..Grains..Legumes",
                     "Grazing.Lands",
                    "Mixed.Species.Hay",
                    "Orchard.Vineyard",
                    "Root.Crops",
                    "Specialty.Row.Crops",
                    "Organic",
                    "Irrigated",
                    "Conservation_Cover",
                    "Conservation_Crop_Rotation",
                    "No_till",
                    "Soil_Carbon_Amendment",
                    "Cover_Crop",
                    "Reduced_Till",
                    "Mulching",
                     "Forage_Harvest_Management",
                     "Prescribed_Grazing",
                    "Row_Arrangement",
                    "Nutrient_Management",
                    "TreeShrub",
                    "Soil_Armor",
                    "Livestock_Integration",
                    "Continuous_Living_Root",
                    "Plant_Diversity",
                    "Minimize_Soil_Disturbance"),
      column_names_gp = gpar(fontsize = 10),  # smaller column names
      row_names_gp = gpar(fontsize =10)      # smaller row names
)