如何更改R中fviz_pca_biplot处圆圈边框线的颜色？

Question

我正在对我的数据进行主成分分析 (PCA)。 这是脚本的最后一部分，我将在其中构建 PCA 双图：

biplot <- fviz_pca_biplot(pca_result,
                # Individuals
                geom.ind = "point",
                fill.ind = Data$Type, col.ind = "black",
                pointshape = 21, pointsize = 2,
                palette = c("#04BF8A","#D7D7D9"),
                addEllipses = TRUE,
                # Variables
                col.var = "black",
                legend.title = "Type",
                repel = TRUE,
                xlim = c(-5,14),
                ylim = c(-3,8),
                ) +

xlab("PC1 (74.5%)") + ylab("PC2 (16.6%)")

biplot + theme_bw()

这是输出：

我不明白为什么椭圆的边框颜色与调色板中指定的颜色不同。

现在，我想更改椭圆的边框颜色（如调色板中指定的那样），或者直接删除边框并仅保留椭圆的填充。

你能告诉我该怎么做吗？

非常感谢您的帮助！

我尝试在 addEllipse = TRUE 字符串之后立即应用 ellipse.border.remove = TRUE，但出现错误：

ggpubr :: ggscatter中的错误（数据= df，x =“x”，y =“y”，颜色=颜色，： 形式参数“ellipse.border.remove”与多个实际参数匹配

Answer 1

我怀疑这是 fviz_pca_biplot() 函数的限制，但潜在的解决方法是“手动”指定颜色，例如

library(factoextra)
#> Loading required package: ggplot2
#> Welcome! Want to learn more? See two factoextra-related books

data(iris)
res.pca <- prcomp(iris[, -5],  scale = TRUE)

# palette works for fill but not for ellipses color
fviz_pca_biplot(res.pca,
                # Individuals
                geom.ind = "point",
                fill.ind = iris$Species,
                col.ind = "black",
                pointshape = 21, pointsize = 2,
                palette = c("#04BF8A","#D7D7D9", "red"),
                addEllipses = TRUE,
                # Variables
                col.var = "black",
                legend.title = "Type",
                repel = TRUE,
                xlim = c(-5,14),
                ylim = c(-3,8),
) +
  xlab("PC1 (74.5%)") +
  ylab("PC2 (16.6%)") +
  theme_bw()
#> Coordinate system already present. Adding new coordinate system, which will
#> replace the existing one.

# fix ellipses color
fviz_pca_biplot(res.pca,
                          # Individuals
                          geom.ind = "point",
                          fill.ind = iris$Species,
                          col.ind = "black",
                          pointshape = 21, pointsize = 2,
                          palette = c("#04BF8A","#D7D7D9", "red"),
                          addEllipses = TRUE,
                          # Variables
                          col.var = "black",
                          legend.title = "Type",
                          repel = TRUE,
                          xlim = c(-5,14),
                          ylim = c(-3,8),
) +
  xlab("PC1 (74.5%)") +
  ylab("PC2 (16.6%)") +
  theme_bw() +
  scale_color_manual(values = c("setosa" = "#04BF8A",
                                "versicolor" = "#D7D7D9",
                                "virginica" = "red"))
#> Coordinate system already present. Adding new coordinate system, which will
#> replace the existing one.

^{创建于 2024-02-21，使用 reprex v2.1.0}

这适用于您的“真实”数据吗？