r - PCA 双图组个体

Question

我的数据中有很多人（n = 600）。我运行 PCA 并想创建变量和个体的 Biplot。我想要由它们的贡献着色的变量。这些人来自两组，我想根据两组对点进行着色。我附上一个小例子。

library(FactoMineR)
library(factoextra)
data(decathlon2)
decathlon2.active <- decathlon2[1:23, 1:10]
head(decathlon2.active[, 1:6])
res.pca <- PCA(decathlon2.active, graph = FALSE)
fviz_pca_biplot(res.pca, col.var="cos", geom = "point") + scale_color_gradient2(low="white", mid="blue", 
                    high="red", midpoint=0.5) + theme_minimal()

res.pca_ind = data.frame(res.pca$ind)
res.pca_ind

问题;

1. 如何将行名 SEBRLE 和 NOOL 涂成红色，其余的涂成黑色
2. 将所有行名分配给 2 个因素中的 1 个（我不介意这是一个例子），并为它们着色。

部分回答；

sub = as.character(rownames(res.pca_ind))
decathlon3 = decathlon2[which(rownames(decathlon2) %in% sub),]

fviz_pca_biplot(res.pca, axes = c(1, 2), geom = c("point", "text"),
            label = "all", invisible = "none", labelsize = 2, pointsize = 2,
            habillage = decathlon3$Competition, addEllipses = FALSE,    ellipse.level = 0.95,
            col.ind = "black", col.ind.sup = "blue", alpha.ind = 1,
            col.var = "steelblue", alpha.var = 1, col.quanti.sup = "blue",
            col.circle = NULL, 
            select.var = list(name = NULL, cos2 = NULL, contrib= NULL), 
            select.ind = list(name = NULL, cos2 = NULL, contrib = NULL),
            jitter = list(what = "label", width = NULL, height = NULL))

然而，在我得到的地方，我正在失去。正如不断出现的那样，我无法找到同时使用 habillage 和 contrib 的 select.var 的方法Error: Continuous value supplied to discrete scale。

Answer 1

如果您不需要图例：

library(factoextra)

point_col = ifelse(rownames(decathlon2.active) %in% c("SEBRLE","NOOL"),
"red","black")

res.pca <- PCA(decathlon2.active, graph = FALSE)
g = fviz_pca_biplot(res.pca, col.var="contrib", geom = "") +
scale_color_gradient2(low="white", mid="blue", high="red", midpoint=0.5) + 
theme_minimal() 
g + geom_point(col = point_col)

如果你需要一个图例，我将包含 sebrle 和 nool 的观察命名为 0，其他命名为 1：

library(ggnewscale)

g$data$group = +(rownames(decathlon2.active) %in% c("SEBRLE","NOOL"))
g + new_scale_color() + 
geom_point(aes(col=factor(group))) + 
scale_color_manual(values = c("black","red"))