GGally与pairs相关关系图_史上最全（一）

作者： 李誉辉

四川大学在读研究生

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 <- ggplot(tips, aes(x = total_bill, fill = sex)) + 
 7  geom_density(show.legend = FALSE)
 8
 9g2 <- ggplot(tips, aes(x = total_bill, fill = sex)) + 
10  geom_histogram(position = position_stack(), show.legend = FALSE) + 
11  facet_grid(rows = vars(time))# 以time变量行分面
12
13g3 <- ggplot(tips, aes(x = total_bill, y = tip, color = sex)) + 
14  geom_point(show.legend = FALSE)
15

1.2

矩阵第2列

 1library(ggplot2)
 2
 3g4 <- ggplot(tips, aes(x = time, y = total_bill, fill = sex)) + 
 4  geom_boxplot(show.legend = FALSE)
 5
 6g5 <- ggplot(tips, aes(x = time, fill = sex)) + 
 7  geom_bar(position = position_stack(), show.legend = FALSE)
 8
 9g6 <- ggplot(tips, aes(x = tip, fill = sex)) + 
10  geom_histogram(position = position_stack(), show.legend = FALSE) + 
11  coord_flip() + 
12  facet_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 <- round(cor(tips$total_bill, tips$tip), 3)
 7tips_female <- as.tibble(tips) %>% filter(sex == "Female") %>% as.data.frame()
 8tips_male <- as.tibble(tips) %>% filter(sex == "Male") %>% as.data.frame()
 9text_2 <- round(cor(tips_female$total_bill, tips_female$tip), 3)
10text_3 <- round(cor(tips_male$total_bill, tips_male$tip), 3)
11mytext <- c(text_1, text_2, text_3)
12mytext <- paste0(c("Cor", "Female", "Male"), ":", mytext)
13mytext <- data.frame(text = mytext,
14                     x = 5,
15                     y = c(6, 4, 2),
16                     stringsAsFactors = FALSE)
17
18g7 <- ggplot(data = mytext[-1, ], aes(x = x, y = y, label = text, color = text)) + 
19  geom_text(show.legend = F) + 
20  geom_text(data = mytext[1,], aes(x = x, y = y, label = text), 
21            color = "black") 
22
23rm(text_1, tips_female, tips_male, text_2, text_3, mytext)
24
25# 第2个图
26g8 <- ggplot(tips, aes(x = time, y = tip, fill = sex)) + 
27  geom_boxplot(show.legend = FALSE) + 
28  coord_flip()
29
30# 第3个图
31g9 <- ggplot(tips, aes(x = tip, fill = sex)) + 
32  geom_density(show.legend = FALSE)
33

1.4

customLayout合并图形

 1library(customLayout)
 2# 创建画布
 3mylay <- lay_new(
 4  mat = matrix(1:9, ncol = 3))
 5
 6plot_list <- list(g1, g2, g3, g4, g5, g6, g7, g8, g9) 
 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 <- ggmatrix(
 4  plots = plot_list, # 绘图对象列表
 5  nrow = 3, ncol = 3, # 行数和列数
 6  xAxisLabels = c("Total Bill", "Time of Day", "Tip"),
 7  yAxisLabels = c("Total Bill", "Time of Day", "Tip"),
 8  byrow = FALSE, # 按列排
 9  title = "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,
 2  upper = 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, ...,
 6  xlab = NULL, ylab = NULL, axisLabels = c("show", "internal", "none"),
 7  columnLabels = colnames(data[columns]), labeller = "label_value",
 8  switch = NULL, showStrips = NULL, legend = NULL,
 9  cardinality_threshold = 15, progress = NULL,
10  legends = 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), 
 5  columns = c("total_bill", "time", "tip"), 
 6  columnLabels = c("Total_Bill(连续变量)", "Time(离散变量)", "Tip(连续变量)"),
 7  title = "变量名指定column")
 8
 9ggpairs(tips, mapping = aes(color = sex), 
10  columns = c(1, 6, 2), 
11  columnLabels = c("Total_Bill(连续变量)", "Time(离散变量)", "Tip(连续变量)"),
12  title = "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), 
 2  columns = c("total_bill", "time", "tip"), 
 3  columnLabels = c("Total_Bill(连续变量)", "Time(离散变量)", "Tip(连续变量)"),
 4  lower = list(
 5    continuous = "cor",
 6    combo = "dot_no_facet" # 没有2个离散变量，不需要discrete参数
 7  ),
 8  upper = list(
 9    continuous = "blank",
10    combo = "blank"
11  ),
12  diag = list(
13    continuous = "blankDiag",
14    discrete = "blankDiag"
15  ),
16  title = "自定义lower\n(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), 
 2  columns = c("total_bill", "time", "sex"), 
 3  columnLabels = c("Total_Bill(连续变量)", "Time(离散变量)", "Sex(离散变量)"),
 4  lower = list(
 5    combo = "dot_no_facet", # 
 6    discrete = "blank"
 7  ),
 8  upper = list(
 9    combo = "blank",
10    discrete = "blank"
11  ),
12  diag = list(
13    continuous = "blankDiag",
14    discrete = "blankDiag"
15  ),
16  title = "自定义lower\n(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), 
 2  columns = c("total_bill", "time", "tip"), 
 3  columnLabels = c("Total_Bill(连续变量)", "Time(离散变量)", "Tip(连续变量)"),
 4  upper = list(
 5    continuous = "density",
 6    combo = "dot_no_facet" # 没有2个离散变量，不需要discrete参数
 7  ),
 8  lower = list(
 9    continuous = "blank",
10    combo = "blank"
11  ),
12  diag = list(
13    continuous = "blankDiag",
14    discrete = "blankDiag"
15  ),
16  title = "自定义upper\n(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), 
 2  columns = c("total_bill", "time", "sex"), 
 3  columnLabels = c("Total_Bill(连续变量)", "Time(离散变量)", "Sex(离散变量)"),
 4  upper = list(
 5    combo = "dot_no_facet", # 
 6    discrete = "ratio"
 7  ),
 8  lower = list(
 9    combo = "blank",
10    discrete = "blank"
11  ),
12  diag = list(
13    continuous = "blankDiag",
14    discrete = "blankDiag"
15  ),
16  title = "自定义upper\n(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), 
 2  columns = c("total_bill", "time", "tip"), 
 3  columnLabels = c("Total_Bill(连续变量)", "Time(离散变量)", "Tip(连续变量)"),
 4  diag  = list(
 5    continuous = "barDiag",
 6    discrete = "blankDiag" #
 7  ),
 8  lower = list(
 9    continuous = "blank",
10    combo = "blank"
11  ),
12  upper = list(
13    continuous = "blank",
14    combo = "blank"
15  ),
16  title = "自定义diag\n(diag$continuous = \"barDiag\", diag$discrete = \"blankDiag\")"
17)

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

2.3.4  mapping 参数

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

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

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

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