pairs在R语言中的含义 r语言pairs函数

作者：李誉辉
四川大学在读研究生
简介
对于多个变量之间的相关关系，常常使用相关关系图来可视化，R自带有pairs()函数，
可以画相关关系图，但是比较复杂，我们先介绍基于ggplot2的GGally包。
等介绍完，再介绍pairs()函数。
1.ggmatrix()
ggmatrix()可以将多个ggplot2绘图对象，按照矩阵进行排列。
1.1
矩阵第1列
1library(ggplot2)
2data(tips, package = "reshape")
3
4head(tips)
5
6g1 
7geom_density(show.legend= FALSE)
8
9g2
10geom_histogram(position= position_stack(),show.legend= FALSE)+
11facet_grid(rows= vars(time))#以time变量行分面
12
13g3
14geom_point(show.legend= FALSE)
15

1.2
矩阵第2列
1library(ggplot2)
2
3g4 
4geom_boxplot(show.legend= FALSE)
5
6g5
7geom_bar(position= position_stack(),show.legend= FALSE)
8
9g6
10geom_histogram(position= position_stack(),show.legend= FALSE)+
11coord_flip() +
12facet_grid(cols= vars(time))
13
1.3
矩阵第3列
1library(ggplot2)
2library(dplyr)
3library(tibble)
4
5# 第一个图
6text_1 
7tips_female% filter(sex == "Female") %>% as.data.frame()
8tips_male % filter(sex == "Male") %>% as.data.frame()
9text_2 
10text_3
11mytext
12mytext
13mytext
14x= 5,
15y= c(6,4, 2),
16stringsAsFactors= FALSE)
17
18g7
19geom_text(show.legend= F)+
20geom_text(data= mytext[1,],aes(x= x,y= y,label= text),
21color= "black")
22
23rm(text_1, tips_female, tips_male, text_2, text_3, mytext)
24
25# 第2个图
26g8
27geom_boxplot(show.legend= FALSE)+
28coord_flip()
29
30# 第3个图
31g9
32geom_density(show.legend= FALSE)
33
1.4
customLayout合并图形
1library(customLayout)
2# 创建画布
3mylay 
4mat = matrix(1:9, ncol = 3))
5
6plot_list 
7
8lay_grid(plot_list, mylay) # ggplot2绘图列表传参，传递到画布mylay
9
10rm(g1, g2, g3, g4, g5, g6, g7, g8, g9, mylay)

1.5
ggmatrix合并图形
1library(GGally)
2
3gg_m 
4plots = plot_list, # 绘图对象列表
5nrow = 3, ncol = 3, # 行数和列数
6xAxisLabels = c("Total Bill", "Time of Day", "Tip"),
7yAxisLabels = c("Total Bill", "Time of Day", "Tip"),
8byrow = FALSE, # 按列排
9title = "ggmatrix合并图形"
10)
11
12# 添加主题
13gg_m + theme_bw()
14
15# 提取子集,只能提取其中一个
16gg_m[1,2]
17
18rm(plot_list, gg_m)


2.ggpairs()
GGally通过添加几个函数来扩展ggplot2，以降低geom与转换数据组合的复杂性。
其中一些功能包括配对图矩阵，散点图矩阵，平行坐标图，生存图，以及绘制网络的几个函数。
2.1
语法及关键参数
语法：
1ggpairs(data, mapping = NULL, columns = 1:ncol(data), title = NULL,
2upper = list(continuous = "cor", combo = "box_no_facet", discrete =
3"facetbar", na = "na"), lower = list(continuous = "points", combo =
4"facethist", discrete = "facetbar", na = "na"), diag = list(continuous =
5"densityDiag", discrete = "barDiag", na = "naDiag"), params = NULL, ...,
6xlab = NULL, ylab = NULL, axisLabels = c("show", "internal", "none"),
7columnLabels = colnames(data[columns]), labeller = "label_value",
8switch= NULL, showStrips = NULL, legend = NULL,
9cardinality_threshold = 15, progress = NULL,
10legends = stop("deprecated"))
关键参数：
mapping, 表示要叠加到x,y上的aes()映射变量，这里是全局映射。
column, 表示选择要绘图的列，可以用变量索引值指定，也可以用变量名指定。
columnLabels, 指定矩阵列名称。
title, xlab, ylab, 表示指定标题和坐标轴名称。
lower,upper,表示指定下三角和上三角的plot类型，列表传参。
diag,表示指定对角线的plot类型，列表传参。
axisLabels, 指定变量名称的显示位置，默认显示在外侧， "internal"则显示在内测，"none"则不显示。
labeller, 表示指定分面标签，
switch, 表示指定分面标签位置，与ggplot2:facet_grid中一致，默认在顶部和右侧， 若switch = "x",则显示在底部和右侧，若switch = "y"则显示在顶部和左侧， 若swith = "both"则显示在底部和左侧。
showStrips, 布尔运算决定是否显示plots的条带，默认NULL只显示顶部和右侧的条带。 TRUE则显示所有的条带，FALSE则不显示所有的条带。
legend, 默认NULL不显示，可以通过theme(legend.position = "bottom")调整图例的位置。 有3种指定图例类型的方式：
长度为2的数字向量，表示给矩阵所在的行和列增加图例。如c(2,3)表示第2行第3列增加图例。
长度为1的数字向量，表示根据矩阵的顺序，给相应的panel添加图例， 如legend=3表示给1行第3列增加图例。
预先使用grab_legend()提取ggplot2对象的图例，然后指定给legend。
cardinality_threshold, 表示允许因子变量的最大因子水平数量，默认最多15个因子水平。NULL则因子变量不会绘图。
progress, 表示是否显示进度条，默认NULL当超过15个plots时显示进度条, 对绘图结果没有任何影响，不需要关注。 TRUE则显示进度条，FALSE则不显示进度条， 也可用ggmatrix_progress()生成进度条，然后指定。
plot类型：
通过5个参数控制plot类型：continuous,combo,discret,na,mapping
continuous, 表示如果变量x,y都是连续的，应该是什么plot。
对于lower和upper参数： 可以是 "point", "smooth","smooth_loess", "density", "cor", "blank"。
对于diag参数: 可以是 "densityDiag", "barDiag", "blankDiag"
combo, 表示如果变量一个连续，一个离散，应该是什么plot。 只能用于lower和upper不能用于diag。 离散变量只能计数，不能映射坐标，所以可能存在坐标翻转。
可以是 "box", "box_no_facet", "dot", "dot_no_facet", "facethist", "facetdensity", "denstrip", "blank"
discrete, 表示2个变量都是离散的，应该是什么plot。
对于upper和lower参数： 可以是： "facetbar", "ratio", "blank"。
对于diag参数: 可以是"barDiag", "blankDiag"。
na, 表示指定变量为na的情况,
对于lower和upper，可以是："na", "blank"。
对于diag,可以是 "naDiag"，"blankDiag"。
mapping, 表示aes()映射。若指定mapping参数，则叠加到x,y上去。
默认 lower = list(continuous = "point", combo = "facetthist", discrete = "facetbar")
默认 upper = list(continuous = "cor", combo = "box_no_facet", discrete = "box")
默认 diag = list(continuous = "density", discrete = "barDiag")
2.2
column及columnLabels
1library(GGally)
2library(ggplot2)
3
4ggpairs(tips, mapping = aes(color = sex),
5columns = c("total_bill", "time", "tip"),
6columnLabels = c("Total_Bill(连续变量)", "Time(离散变量)", "Tip(连续变量)"),
7title = "变量名指定column")
8
9ggpairs(tips, mapping = aes(color = sex),
10columns = c(1, 6, 2),
11columnLabels = c("Total_Bill(连续变量)", "Time(离散变量)", "Tip(连续变量)"),
12title = "索引值指定column")


2.3
lower,upper, diag
2.3.1自定义lower
一个离散变量，lower的discrete参数无效。
1ggpairs(tips, mapping = aes(color = day),
2columns = c("total_bill", "time", "tip"),
3columnLabels = c("Total_Bill(连续变量)", "Time(离散变量)", "Tip(连续变量)"),
4lower = list(
5continuous = "cor",
6combo = "dot_no_facet"# 没有2个离散变量，不需要discrete参数
7),
8upper = list(
9continuous = "blank",
10combo = "blank"
11),
12diag = list(
13continuous = "blankDiag",
14discrete = "blankDiag"
15),
16title = "自定义lowern(lower$continuous = "cor", lower$combo = "dot_no_facet")"
17)

两个离散变量，lower的continuous参数无效。
1ggpairs(tips, mapping = aes(color = day),
2columns = c("total_bill", "time", "sex"),
3columnLabels = c("Total_Bill(连续变量)", "Time(离散变量)", "Sex(离散变量)"),
4lower = list(
5combo = "dot_no_facet", #
6discrete = "blank"
7),
8upper = list(
9combo = "blank",
10discrete = "blank"
11),
12diag = list(
13continuous = "blankDiag",
14discrete = "blankDiag"
15),
16title = "自定义lowern(lower$combo = "dot_no_facet",lower$discrete = "blank" )"
17)

2.3.2自定义upper
一个离散变量，upper的discrete参数无效。
1ggpairs(tips, mapping = aes(color = day),
2columns = c("total_bill", "time", "tip"),
3columnLabels = c("Total_Bill(连续变量)", "Time(离散变量)", "Tip(连续变量)"),
4upper = list(
5continuous = "density",
6combo = "dot_no_facet"# 没有2个离散变量，不需要discrete参数
7),
8lower = list(
9continuous = "blank",
10combo = "blank"
11),
12diag = list(
13continuous = "blankDiag",
14discrete = "blankDiag"
15),
16title = "自定义uppern(upper$continuous = "density", upper$combo = "dot_no_facet")"
17)

两个离散变量，upper的continuous参数无效。
1ggpairs(tips, mapping = aes(color = day),
2columns = c("total_bill", "time", "sex"),
3columnLabels = c("Total_Bill(连续变量)", "Time(离散变量)", "Sex(离散变量)"),
4upper = list(
5combo = "dot_no_facet", #
6discrete = "ratio"
7),
8lower = list(
9combo = "blank",
10discrete = "blank"
11),
12diag = list(
13continuous = "blankDiag",
14discrete = "blankDiag"
15),
16title = "自定义uppern(lower$combo = "dot_no_facet",upper$discrete = "ratio" )"
17)

2.3.3自定义diag
diag没有combo参数。
1ggpairs(tips, mapping = aes(color = day),
2columns = c("total_bill", "time", "tip"),
3columnLabels = c("Total_Bill(连续变量)", "Time(离散变量)", "Tip(连续变量)"),
4diag = list(
5continuous = "barDiag",
6discrete = "blankDiag"#
7),
8lower = list(
9continuous = "blank",
10combo = "blank"
11),
12upper = list(
13continuous = "blank",
14combo = "blank"
15),
16title = "自定义diagn(diag$continuous = "barDiag", diag$discrete = "blankDiag")"
17)

1ggpairs(tips, mapping = aes(color = day),
2columns = c("total_bill", "time", "sex"),
3columnLabels = c("Total_Bill(连续变量)", "Time(离散变量)", "Sex(离散变量)"),
4diag = list(
5continuous = "barDiag", #
6discrete = "barDiag"
7),
8lower = list(
9discrete = "blank",
10combo = "blank"
11),
12upper = list(
13discrete = "blank",
14combo = "blank"
15),
16title = "自定义diagn(lower$continuous = "barDiag",diag$barDiag = "barDiag" )"
17)

2.3.4mapping参数
1library(ggplot2)
2library(GGally)
3data(tips, package = "reshape")
4
5ggpairs(tips,
6columns = c("total_bill", "time", "tip"),
7columnLabels = c("Total_Bill(连续变量)", "Time(离散变量)", "Tip(连续变量)"),
8title = "无mapping"
9)

1ggpairs(tips,
2columns = c("total_bill", "time", "tip"),
3columnLabels = c("Total_Bill(连续变量)", "Time(离散变量)", "Tip(连续变量)"),
4lower = list(mapping = aes(color = time)),
5title = "自定义lower(lower$mapping = "time")"# 局部映射
6)

1ggpairs(tips,
2columns = c("total_bill", "tip", "size"),
3columnLabels = c("Total_Bill(连续变量)", "Tip(连续变量)", "Size(连续变量)"),
4lower = list(
5continuous = "cor",
6mapping = aes(color = sex)
7),
8upper = list(
9continuous = "cor",
10mapping = aes(color = smoker)
11),
12diag = list(
13continuous = "barDiag",
14mapping = aes(color = time)
15),
16title = "自定义lower,upper,diagn(下三角颜色为sex,上三角颜色为smoker,对角颜色为time)"
17)

2.3.5同时指定lower,upper,diag
2个连续变量，1个离散变量。
1ggpairs(tips, mapping = aes(color = day),
2columns = c("total_bill", "tip", "time"),
3columnLabels = c("Total_Bill(连续变量)", "Tip(连续变量)", "Time(离散变量)"),
4lower = list(
5continuous = "cor",
6combo = "dot_no_facet"# 没有2个离散变量，不需要discrete参数
7),
8upper = list(
9continuous = "density",
10combo = "dot_no_facet"# 没有2个离散变量，不需要discrete参数
11),
12diag = list(
13continuous = "barDiag",
14discrete = "blankDiag"#
15),
16title = "自定义lower,upper,diag(两个连续变量，一个离散变量)"
17)

1个连续变量，2个离散变量。
1ggpairs(tips, mapping = aes(color = day),
2columns = c("total_bill", "time", "sex"),
3columnLabels = c("Total_Bill(连续变量)", "Time(离散变量)", "Sex(离散变量)"),
4lower = list(
5combo = "dot_no_facet", #
6discrete = "blank"
7),
8upper = list(
9combo = "dot_no_facet", #
10discrete = "ratio"
11),
12diag = list(
13continuous = "barDiag", #
14discrete = "barDiag"
15),
16title = "自定义lower,upper,diag(一个连续变量，两个离散变量)"
17)