R|UpSet-集合可視化

介紹一個R包UpSetR，專門用來集合可視化，當多集合的韋恩圖不容易看的時候，就是它大展身手的時候了。

一、R包及數據

#安裝及載入R包#install.packages("UpSetR")library(UpSetR) #載入數據集data <- read.csv("upSet.csv",header=TRUE)#先大致瀏覽一下該數據集,數據集太長，就只看前幾列head(data[,1:6],6)#View(data) #彈出窗口，可查看數據

二、upset()函數

使用UpsetR包裡面的upset()函數繪製集合可視化圖形。

1）基本參數

upset(data, sets = c("Action", "Adventure", "Comedy", "Drama", "Fantasy" , "Children","Crime"),#查看特定的幾個集合 mb.ratio = c(0.55, 0.45),#控制上方條形圖以及下方點圖的比例 order.by = "freq", #如何排序，這裡freq表示從大到小排序展示 keep.order = TRUE, #keep.order按照sets參數的順序排序 number.angles = 30, #調整柱形圖上數字角度 point.size = 2, line.size = 1, #點和線的大小 mainbar.y.label = "Genre Intersections", sets.x.label = "Movies Per Genre", #坐標軸名稱 text.scale = c(1.3, 1.3, 1, 1, 1.5, 1)) #六個數字，分別控制c(intersection size title, intersection size tick labels, set size title, set size tick labels, set names, numbers above bars)

2）queries參數

queries參數分為四個部分：query, param, color, active；

query: 指定哪個query，UpSetR有內置，也可以自定義；

param: list, query作用於哪個交集

color：每個query都是一個list，裡面可以設置顏色,沒設置的話將調用包里默認的調色板；

active：被指定的條形圖：TRUE顯示顏色，FALSE在條形圖頂端顯示三角形；

upset(data, main.bar.color = "black", queries = list(list(query = intersects, #UpSetR 內置的intersects queryparams = list("Drama"), ##指定作用的交集color = "red", ##設置顏色，未設置會調用默認調色板active = F, # TRUE：條形圖被顏色覆蓋，FALSE：條形圖頂端顯示三角形query.name = "Drama"), # 添加query圖例list(query = intersects, params = list("Action", "Drama"), active = T,query.name = "Emotional action"), list(query = intersects, params = list("Drama", "Comedy", "Action"), color = "orange", active = T)),query.legend = "top")

3）attribute.plots參數

添加屬性圖，內置有柱形圖、散點圖、熱圖等

3.1 添加柱形圖和散點圖

upset(data, main.bar.color = "black", queries = list(list(query = intersects, params = list("Drama"), color = "red", active = F, query.name = "Drama"),list(query = intersects, params = list("Action", "Drama"), active = T,query.name = "Emotional action"), list(query = intersects, params = list("Drama", "Comedy", "Action"), color = "orange", active = T)), attribute.plots = list(gridrows = 45, #添加屬性圖plots = list(list(plot = scatter_plot, #散點圖 x = "ReleaseDate", y = "AvgRating", #橫縱軸的變數queries = T), #T 則顯示出上面queries定義的顏色list(plot = histogram, x = "ReleaseDate", queries = F)), ncols = 2), # 添加的圖分兩列query.legend = "top") #query圖例在最上方

3.2 添加箱線圖

每次最多添加兩個箱線圖

upset(movies, boxplot.summary = c("AvgRating", "ReleaseDate"))

3.3 添加密度曲線圖

因默認屬性圖中沒有密度曲線，需要自定義plot函數

#自定義密度曲線another.plot <- function(data, x, y) { data$decades <- round_any(as.integer(unlist(data[y])), 10, ceiling) data <- data[which(data$decades >= 1970), ] myplot <- (ggplot(data, aes_string(x = x)) + geom_density(aes(fill = factor(decades)), alpha = 0.4) + theme(plot.margin = unit(c(0, 0, 0, 0), "cm"), legend.key.size = unit(0.4, "cm")))}

upset(data, main.bar.color = "black", mb.ratio = c(0.5, 0.5), queries = list(list(query = intersects, params = list("Drama"), color = "red", active = F), list(query = intersects, params = list("Action", "Drama"), active = T), list(query = intersects, params = list("Drama", "Comedy", "Action"), color = "orange", active = T)), attribute.plots = list(gridrows = 50, plots = list(list(plot = histogram, x = "ReleaseDate", queries = F), list(plot = scatter_plot, x = "ReleaseDate", y = "AvgRating", queries = T), list(plot = another.plot, x = "AvgRating", y = "ReleaseDate", queries = F)), ncols = 3))

三、參考資料

hms-dbmi/UpSetR

Index of /web/packages/UpSetR/vignettes