安装

library(UpSetR)
#导入数据
df <- list(
  A = c(1, 2, 3, 4, 5, 6, 8, 12, 13), 
  B = c(1, 2, 4, 5, 7, 10), 
  C = c(1, 5, 6, 7, 8, 9, 10, 11, 13),
  D = c(1, 2, 5, 8, 10, 13))

绘制图形

upset(fromList(df))

UpSetR

library(VennDiagram) 
venn<-venn.diagram(df,filename=NULL,
                   col ="transparent",
                   fill=c('green','#E41A1C','yellow','#0000CD'),
                   alpha=0.6,
                   category = c('A','B','C','D'),
                   fontfamily = "serif",
                   font="3", fontface = "bold")
grid.draw(venn)

Veen

?UpSetR #查看UpSetR包的绘图函数及参数

Description
Visualization of set intersections using novel UpSet matrix design.

Usage
upset(data, nsets = 5, nintersects = 40, sets = NULL,
  keep.order = F, set.metadata = NULL, intersections = NULL,
  matrix.color = "gray23", main.bar.color = "gray23",
  mainbar.y.label = "Intersection Size", mainbar.y.max = NULL,
  sets.bar.color = "gray23", sets.x.label = "Set Size",
  point.size = 2.2, line.size = 0.7, mb.ratio = c(0.7, 0.3),
  expression = NULL, att.pos = NULL, att.color = main.bar.color,
  order.by = c("freq", "degree"), decreasing = c(T, F),
  show.numbers = "yes", number.angles = 0, group.by = "degree",
  cutoff = NULL, queries = NULL, query.legend = "none",
  shade.color = "gray88", shade.alpha = 0.25, matrix.dot.alpha = 0.5,
  empty.intersections = NULL, color.pal = 1, boxplot.summary = NULL,
  attribute.plots = NULL, scale.intersections = "identity",
  scale.sets = "identity", text.scale = 1, set_size.angles = 0,
  set_size.show = FALSE, set_size.numbers_size = NULL,
  set_size.scale_max = NULL)
Arguments
data    
Data set

nsets   
Number of sets to look at

nintersects 
Number of intersections to plot. If set to NA, all intersections will be plotted.

sets    
Specific sets to look at (Include as combinations. Ex: c("Name1", "Name2"))

keep.order  
Keep sets in the order entered using the sets parameter. The default is FALSE, which orders the sets by their sizes.

set.metadata    
Metadata that offers insight to an attribute of the sets. Input should be a data frame where the first column is set names, and the remaining columns are attributes of those sets. To learn how to use this parameter it is highly suggested to view the set metadata vignette. The link can be found on the package's GitHub page.

intersections   
Specific intersections to include in plot entered as a list of lists. Ex: list(list("Set name1", "Set name2"), list("Set name1", "Set name3")). If data is entered into this parameter the only data shown on the UpSet plot will be the specific intersections listed.

matrix.color    
Color of the intersection points

main.bar.color  
Color of the main bar plot

mainbar.y.label 
The y-axis label of the intersection size bar plot

mainbar.y.max   
The maximum y value of the intersection size bar plot scale. May be useful when aligning multiple UpSet plots horizontally.

sets.bar.color  
Color of set size bar plot

sets.x.label    
The x-axis label of the set size bar plot

point.size  
Size of points in matrix plot

line.size   
Width of lines in matrix plot

mb.ratio    
Ratio between matrix plot and main bar plot (Keep in terms of hundredths)

expression  
Expression to subset attributes of intersection or element query data. Enter as string (Ex: "ColName > 3")

att.pos 
Position of attribute plot. If NULL or "bottom" the plot will be at below UpSet plot. If "top" it will be above UpSet plot

att.color   
Color of attribute histogram bins or scatterplot points for unqueried data represented by main bars. Default set to color of main bars.

order.by    
How the intersections in the matrix should be ordered by. Options include frequency (entered as "freq"), degree, or both in any order.

decreasing  
How the variables in order.by should be ordered. "freq" is decreasing (greatest to least) and "degree" is increasing (least to greatest)

show.numbers    
Show numbers of intersection sizes above bars

number.angles   
The angle of the numbers atop the intersection size bars

group.by    
How the data should be grouped ("degree" or "sets")

cutoff  
The number of intersections from each set (to cut off at) when aggregating by sets

queries 
Unified query of intersections, elements, and custom row functions. Entered as a list that contains a list of queries. query is the type of query being conducted. params are the parameters of the query (if any). color is the color of the points on the plot that will represent the query. If no color is selected one will be provided automatically. active takes TRUE or FALSE, and if TRUE, it will overlay the bars present with the results from the query. If FALSE a tick mark will indicate the intersection size. See examples section on how to do this.

query.legend    
Position query legend on top or bottom of UpSet plot

shade.color 
Color of row shading in matrix

shade.alpha 
Transparency of shading in matrix

matrix.dot.alpha    
Transparency of the empty intersections points in the matrix

empty.intersections 
Additionally display empty sets up to nintersects

color.pal   
Color palette for attribute plots

boxplot.summary 
Boxplots representing the distribution of a selected attribute for each intersection. Select attributes by entering a character vector of attribute names (e.g. c("Name1", "Name2")). The maximum number of attributes that can be entered is 2.

attribute.plots 
Create custom ggplot using intersection data represented in the main bar plot. Prior to adding custom plots, the UpSet plot is set up in a 100 by 100 grid. The attribute.plots parameter takes a list that contains the number of rows that should be allocated for the custom plot, and a list of plots with specified positions. nrows is the number of rows the custom plots should take up. There is already 100 allocated for the custom plot. plots takes a list that contains a function that returns a custom ggplot and the x and y aesthetics for the function. ncols is the number of columns that your ggplots should take up. See examples for how to add custom ggplots.

scale.intersections 
The scale to be used for the intersection sizes. Options: "identity", "log10", "log2"

scale.sets  
The scale to be used for the set sizes. Options: "identity", "log10", "log2"

text.scale  
Numeric, value to scale the text sizes, applies to all axis labels, tick labels, and numbers above bar plot. Can be a universal scale, or a vector containing individual scales in the following format: c(intersection size title, intersection size tick labels, set size title, set size tick labels, set names, numbers above bars)

set_size.angles 
Numeric, angle to rotate the set size plot x-axis text

set_size.show   
Logical, display the set sizes on the set size bar chart

set_size.numbers_size   
If set_size.show is TRUE, adjust the size of the numbers

set_size.scale_max  
Increase the maximum of set size scale