如何根据R中的不同变量在图中使用多个符号？

Question

我已经创建了一个PCA，用于从位于四个基板上的四个位置收集的个体进行测量，重复三次。我有性别（男性或女性）和“核型”（具有三种可能类别的因素）和计算每个人的前两个PC分数。

我想制作一个情节，其中男性和女性有不同的符号，符号的颜色取决于karotype。我用下面的代码创建了一个图，它为我提供了一个符号颜色编码的三个核型，并在男性和女性周围放置了95％的信心。

如何更改每个性别的符号并保持颜色依赖于karytype？我也想在传奇中反映这一点。

最后一个问题。是否可以为每个PC（不是每个人）添加一个箭头，类似于在排序图中找到的箭头？

示例数据：

test <- structure(list(Location = structure(c(1L, 1L, 1L, 1L, 1L, 1L, 
1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 
1L, 1L, 1L), .Label = c("Kampinge", "Kaseberga", "Molle", "Steninge"
), class = "factor"), Substrate = structure(c(1L, 1L, 1L, 1L, 
1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 
1L, 1L, 1L, 2L, 2L), .Label = c("Kampinge", "Kaseberga", "Molle", 
"Steninge"), class = "factor"), Replicate = structure(c(1L, 1L, 
1L, 1L, 1L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 3L, 3L, 3L, 3L, 3L, 3L, 
3L, 3L, 3L, 3L, 3L, 1L, 1L), .Label = c("1", "2", "3"), class = "factor"), 
    Sex = structure(c(2L, 2L, 2L, 1L, 1L, 2L, 2L, 1L, 1L, 2L, 
    2L, 2L, 2L, 1L, 2L, 1L, 1L, 2L, 1L, 2L, 1L, 2L, 2L, 2L, 2L
    ), .Label = c("Female", "Male"), class = "factor"), Karyotype = structure(c(3L, 
    4L, 3L, 3L, 4L, 3L, 4L, 3L, 4L, 3L, 3L, 3L, 3L, 3L, 2L, 4L, 
    3L, 3L, 4L, 4L, 3L, 4L, 3L, 4L, 3L), .Label = c("", "BB", 
    "BD", "DD"), class = "factor"), Wing_Length = c(1439L, 1224L, 
    1558L, 1508L, 1286L, 1560L, 1377L, 1486L, 1638L, 1475L, 1703L, 
    1726L, 1668L, 1405L, 1737L, 1419L, 1530L, 1508L, 1525L, 1326L, 
    1609L, 1357L, 1830L, 1476L, 1661L), Leg_Length = c(465L, 
    357L, 610L, 415L, 343L, 560L, 435L, 390L, 425L, 514L, 693L, 
    695L, 657L, 454L, 661L, 382L, 431L, 531L, 435L, 387L, 407L, 
    414L, 752L, 524L, 650L), Development_Time = c(15, 15, 12, 
    12, 12, 12, 12, 12, 12, 15, 15, 15, 15, 15, 15, 15, 11, 12, 
    14, 12, 14, 14, 14, 11, 11), PC1 = c(-281.031806232855, -515.247908786317, 
    -96.7283446465637, -260.171340782501, -476.664849753781, 
    -127.267190895631, -347.839240839062, -293.08530374415, -154.026702195308, 
    -221.98257463847, 67.7504074590983, 86.6778734586525, 17.8073498265326, 
    -314.171132928964, 73.3068216627556, -349.616320093329, -233.030545551831, 
    -185.761623361004, -234.30046275676, -417.754317941649, -187.820500930148, 
    -376.653043663908, 203.025275308178, -214.80078992031, 7.94703091626344
    ), PC2 = c(-78.3082792875783, -133.370219905995, -113.211488986839, 
    4.31036861466361, -82.8593541869054, -73.5708675263244, -95.0643731443612, 
    9.37702847686542, 80.0290301136235, -92.8061497557789, -83.8731164047719, 
    -70.6537733486393, -78.706783632851, -91.6793310834752, -37.5144466525303, 
    -27.4637667171696, 6.14809390611532, -84.6794844768708, -0.127837123829732, 
    -90.9556028004192, 75.2353710655562, -91.7834027435658, -47.669385541585, 
    -99.8362257341741, -77.8269478596591)), .Names = c("Location", 
"Substrate", "Replicate", "Sex", "Karyotype", "Wing_Length", 
"Leg_Length", "Development_Time", "PC1", "PC2"), row.names = c(1L, 
2L, 3L, 4L, 5L, 6L, 7L, 8L, 9L, 11L, 12L, 13L, 16L, 17L, 18L, 
19L, 20L, 21L, 22L, 23L, 24L, 25L, 26L, 30L, 31L), class = "data.frame")

## Plot
par(mfrow=c(1,1), mar=c(4,4,2,1), pty = "s")
plot(test$PC1, test$PC2, xlab="PC1", ylab="PC2", pch=16, col=as.numeric(test[,"Karyotype"]), 
     xlim = c(-1000, 1000), ylim = c(-250, 250), las=1, cex.lab = 1.5, cex.axis = 1.25, main = NULL)
ordiellipse(test[,9:10], test$Sex, conf=0.95, col="black", cex=1.75, label=TRUE)
legend("bottomright", pch=16, col=unique(as.numeric(test[,"Karyotype"])), legend=unique(test[,"Karyotype"]), cex = 1.75)

Answer 1

将您的pch绘图参数替换为：

pch=ifelse(test$Sex=='Male',15,19)

Answer 2

尝试使用ggplot：

library(ggplot2)
ggplot(test, aes(x=PC1, y=PC2, color=Karyotype, shape=Sex, group=Sex))+geom_point(size=5)+stat_ellipse()