在 ggbiplot pca 中更改圖例和形狀

Question

你能幫我處理我的 pca 嗎？ 我想改變形狀，使每個物種都有不同的顏色，每個物種的所有 2-3 個生物都有 2-3 個不同的符號。 它應該是這樣的：在此處輸入圖像描述

到目前為止，我嘗試了以下代碼：

setwd("~/Schwarze Johannisbeeren/SJ Wein mit nicht Sc/PCA/stackoverflow frage")
results = read.csv("results.csv", sep = ";", encoding = "UTF-8", header=TRUE, check.names=FALSE)


results.pca <- prcomp(results[,c(3:7)],       
                    center = TRUE,
                    scale. = TRUE)

#grouping by organism
results.organism <- results[, 1]

#by species
results.species <- results[, 2]


summary(results.pca)


library(ggplot2)
library(ggbiplot)


ggbiplot(results.pca, alpha=0, obs.scale = 1, var.scale = 1 ,ellipse = TRUE,ellipse.prob=0.68, circle = F, varname.size=0, 
         var.axes = F, groups=results$species) +
  theme_bw()+
  geom_point(aes( colour=factor(results.species)), size=2)+
scale_shape_manual(values= c("Mt1"= 1,  "Mt2" =2, "Al1"= 1, "Al2" =2, "Bg1" =1, "Bg2"=2, "Bg3" =3, "Cs1"= 1, "Cs2" =2, "Cs3" =3, "Df1"= 1, "Df2" =2, "Df3" =3))+
                     
  #scale_color_brewer(name= "organism", type = "qual", palette = 2)+
  #scale_x_continuous (limits = c (-1, 9))+   
  theme(axis.text.x = element_text(size = 12, colour = "black", vjust = 0.5, hjust = 1, face= "bold"), 
        axis.title.y = element_text(size = 12, face = "bold"),
        axis.title.x = element_text(size = 12, face = "bold"),
        axis.text.y = element_text(colour = "black", size = 12, face = "bold"))

那是我的數據

> results
   organism species  lactones cyanides alcohols  ethers   acids
1       Mt1      Mt 23435.167    166.4 137653.9  4040.1 1131.52
2       Mt1      Mt 23303.111    168.9 153511.0  4529.1 1148.52
3       Mt1      Mt 22340.556    176.6 150719.9  3255.8 1200.88
4       Mt2      Mt 51519.222    175.9 173401.1  3890.1 1196.12
5       Mt2      Mt 48824.500    166.5 171614.4  3694.1 1132.20
6       Mt2      Mt 50427.278    165.4 168865.1  3693.2 1124.72
7       Al1      Al 25260.222    162.0 211737.4  9563.9 1101.60
8       Al1      Al 23177.556    161.5 199886.7 10403.3 1098.20
9       Al1      Al 27903.000    156.2 240088.4 11897.1 1062.16
10      Al2      Al  5993.722    180.4 289334.9  6673.3 1226.72
11      Al2      Al  7307.389    169.7 275631.1  8333.4 1153.96
12      Al2      Al  9419.167    147.5 277924.5  9622.2 1003.00
13      Bg1      Bg 58216.944    132.4  92275.3  4099.5  900.32
14      Bg1      Bg 69860.222    147.4 105654.9  4080.6 1002.32
15      Bg1      Bg 72809.333    145.8 111731.3  4014.6  991.44
16      Bg2      Bg 51584.611    142.9 105548.2  6450.1  971.72
17      Bg2      Bg 57738.056    141.2 117728.9  6332.4  960.16
18      Bg2      Bg 53356.056    142.7 110260.2  6506.2  970.36
19      Bg3      Bg 41983.389    130.8 103799.4  4781.8  889.44
20      Bg3      Bg 46930.722    148.3 113944.6  5151.6 1008.44
21      Bg3      Bg 49487.611    139.4 121976.5  5318.3  947.92
22      Cs1      Cs  7155.056    161.6 221538.8  8356.0 1098.88
23      Cs1      Cs  8153.611    151.0 179823.0  7961.2 1026.80
24      Cs1      Cs  7445.722    168.6 176978.0  8196.5 1146.48
25      Cs2      Cs 10771.556    126.4 144314.1  8634.6  859.52
26      Cs2      Cs 12239.556    142.6 142913.7  9471.9  969.68
27      Cs2      Cs 13788.611    136.1 131506.7  9390.4  925.48
28      Cs3      Cs 12082.111    152.0 171730.0  6259.6 1033.60
29      Cs3      Cs 14331.556    143.3 141748.7  7532.8  974.44
30      Cs3      Cs 14123.056    158.2 150303.0  7755.8 1075.76
31      Df1      Df 26906.778    156.2 310203.9  5505.5 1062.16
32      Df1      Df 20689.111    163.5 214322.9  5315.6 1111.80
33      Df1      Df 22872.722    154.1 197572.9  4627.7 1047.88
34      Df2      Df 18838.222    159.2 125167.6 12372.9 1082.56
35      Df2      Df 18218.667    155.8 127077.2 11182.0 1059.44
36      Df2      Df 18545.389    156.2 154400.4 10543.6 1062.16
37      Df3      Df 19924.111    156.4 199472.6  4452.3 1063.52
38      Df3      Df 22504.056    158.0 196343.0  3994.1 1074.40
39      Df3      Df 16907.278    151.5 185052.9  4084.6 1030.20
>

順便說一下，軸標簽是否可以只使用 PC1( x %) 而不是 PC1(x % explained var.)？

Answer 1

實現您想要的結果的一種方法是首先創建形狀和調色板，其中 map 有機體名稱為形狀和 colors。其次，在您的geom_point內通過添加一個包含我使用dplyr::bind_cols的organism的列來擴展數據。 這樣做允許 map organism的shape和color aes。 最后，使用scale_color_discrete(guide = "none")去除組的顏色圖例，並通過ggnewscale::new_scale_color和scale_color_manual添加第二個色標：

注意：軸標題的簡單修復是使用+labs(x =..., y =...)手動設置它們。

library(ggplot2)
library(ggbiplot)

pal_shape <- gsub("^.*?(.)$", "\\1", results$organism)
pal_shape <- scales::shape_pal()(3)[as.integer(pal_shape)]
names(pal_shape) <- results$organism

pal_color <- gsub("^(.*?).$", "\\1", results$organism)
pal_color <- setNames(scales::hue_pal()(5), sort(unique(results$species)))[pal_color]
names(pal_color) <- results$organism

ggbiplot(results.pca,
  alpha = 0, obs.scale = 1, var.scale = 1, ellipse = TRUE, ellipse.prob = 0.68, circle = F, varname.size = 0,
  var.axes = F, groups = results$species
) +
  scale_color_discrete(guide = "none") +
  ggnewscale::new_scale_color() +
  geom_point(data = ~ dplyr::bind_cols(.x, organism = results$organism), 
             aes(shape = organism, colour = organism), 
             size = 2) +
  scale_shape_manual(values = pal_shape) +
  scale_color_manual(values = pal_color) +
  theme_bw() +
  theme(
    axis.text.x = element_text(size = 12, colour = "black", vjust = 0.5, hjust = 1, face = "bold"),
    axis.title.y = element_text(size = 12, face = "bold"),
    axis.title.x = element_text(size = 12, face = "bold"),
    axis.text.y = element_text(colour = "black", size = 12, face = "bold")
  )

數據

results <- structure(list(organism = c(
  "Mt1", "Mt1", "Mt1", "Mt2", "Mt2",
  "Mt2", "Al1", "Al1", "Al1", "Al2", "Al2", "Al2", "Bg1", "Bg1",
  "Bg1", "Bg2", "Bg2", "Bg2", "Bg3", "Bg3", "Bg3", "Cs1", "Cs1",
  "Cs1", "Cs2", "Cs2", "Cs2", "Cs3", "Cs3", "Cs3", "Df1", "Df1",
  "Df1", "Df2", "Df2", "Df2", "Df3", "Df3", "Df3"
), species = c(
  "Mt",
  "Mt", "Mt", "Mt", "Mt", "Mt", "Al", "Al", "Al", "Al", "Al", "Al",
  "Bg", "Bg", "Bg", "Bg", "Bg", "Bg", "Bg", "Bg", "Bg", "Cs", "Cs",
  "Cs", "Cs", "Cs", "Cs", "Cs", "Cs", "Cs", "Df", "Df", "Df", "Df",
  "Df", "Df", "Df", "Df", "Df"
), lactones = c(
  23435.167, 23303.111,
  22340.556, 51519.222, 48824.5, 50427.278, 25260.222, 23177.556,
  27903, 5993.722, 7307.389, 9419.167, 58216.944, 69860.222, 72809.333,
  51584.611, 57738.056, 53356.056, 41983.389, 46930.722, 49487.611,
  7155.056, 8153.611, 7445.722, 10771.556, 12239.556, 13788.611,
  12082.111, 14331.556, 14123.056, 26906.778, 20689.111, 22872.722,
  18838.222, 18218.667, 18545.389, 19924.111, 22504.056, 16907.278
), cyanides = c(
  166.4, 168.9, 176.6, 175.9, 166.5, 165.4, 162,
  161.5, 156.2, 180.4, 169.7, 147.5, 132.4, 147.4, 145.8, 142.9,
  141.2, 142.7, 130.8, 148.3, 139.4, 161.6, 151, 168.6, 126.4,
  142.6, 136.1, 152, 143.3, 158.2, 156.2, 163.5, 154.1, 159.2,
  155.8, 156.2, 156.4, 158, 151.5
), alcohols = c(
  137653.9, 153511,
  150719.9, 173401.1, 171614.4, 168865.1, 211737.4, 199886.7, 240088.4,
  289334.9, 275631.1, 277924.5, 92275.3, 105654.9, 111731.3, 105548.2,
  117728.9, 110260.2, 103799.4, 113944.6, 121976.5, 221538.8, 179823,
  176978, 144314.1, 142913.7, 131506.7, 171730, 141748.7, 150303,
  310203.9, 214322.9, 197572.9, 125167.6, 127077.2, 154400.4, 199472.6,
  196343, 185052.9
), ethers = c(
  4040.1, 4529.1, 3255.8, 3890.1,
  3694.1, 3693.2, 9563.9, 10403.3, 11897.1, 6673.3, 8333.4, 9622.2,
  4099.5, 4080.6, 4014.6, 6450.1, 6332.4, 6506.2, 4781.8, 5151.6,
  5318.3, 8356, 7961.2, 8196.5, 8634.6, 9471.9, 9390.4, 6259.6,
  7532.8, 7755.8, 5505.5, 5315.6, 4627.7, 12372.9, 11182, 10543.6,
  4452.3, 3994.1, 4084.6
), acids = c(
  1131.52, 1148.52, 1200.88,
  1196.12, 1132.2, 1124.72, 1101.6, 1098.2, 1062.16, 1226.72, 1153.96,
  1003, 900.32, 1002.32, 991.44, 971.72, 960.16, 970.36, 889.44,
  1008.44, 947.92, 1098.88, 1026.8, 1146.48, 859.52, 969.68, 925.48,
  1033.6, 974.44, 1075.76, 1062.16, 1111.8, 1047.88, 1082.56, 1059.44,
  1062.16, 1063.52, 1074.4, 1030.2
)), class = "data.frame", row.names = c(
  "1",
  "2", "3", "4", "5", "6", "7", "8", "9", "10", "11", "12", "13",
  "14", "15", "16", "17", "18", "19", "20", "21", "22", "23", "24",
  "25", "26", "27", "28", "29", "30", "31", "32", "33", "34", "35",
  "36", "37", "38", "39"
))