在 PCA 图中命名样本

Question

我有一个包含大量数据的 PCA 图，我想确定哪些样本是异常值。当我使用

geom.ind = c("text")

那么文字太多，我什么都看不懂。

这是一个最小的可重现示例。（我已经在这里使用它但答案只能手动工作而且我真的有一个很棒的数据框）

dataframe <- data_frame("c1"=c(78,89,0),"c2"=c(89,89,34),"c3"=c(56,0,4))
row.names(dataframe) <- c("name1","name2","name3")

sub <- PCA(dataframe)

pca <- fviz_pca_ind(sub, pointsize = "cos2", 
             pointshape = 21, fill = "#E7B800",
             repel = TRUE, # Avoid text overlapping (slow if many points)
             geom = c("text","point"), 
             xlab = "PC1", ylab = "PC2",label = row.names(dataframe)
             )

interactive <- ggplotly(pca,dynamicTicks = T,tooltip = c("x","y",label = list))

如您所见，我尝试使用 ggplotly() 函数来完成，但这不起作用。

我想在我的绘图中识别样本名称 (name1,name2,name3)。我怎样才能为一个伟大的数据集做到这一点？

非常感谢您

Answer 1

您可以使用以下代码

library(tidyverse)
library("factoextra")
library(plotly)
library(FactoMineR)

dataframe <- data_frame("c1"=c(78,89,0),"c2"=c(89,89,34),"c3"=c(56,0,4))
row.names(dataframe) <- c("name1","name2","name3")

sub <- PCA(dataframe)

pca <- fviz_pca_ind(sub, pointsize = "cos2", 
                    pointshape = 21, fill = "#E7B800",
                    repel = TRUE, # Avoid text overlapping (slow if many points)
                    geom = c("text","point"), 
                    xlab = "PC1", ylab = "PC2",label = c("ind")
)

interactive <- ggplotly(pca,tooltip = c("x","y","colour"))

bggly <- plotly_build(interactive)
bggly$x$data[[1]]$text <- 
  with(pca$data, paste0("name: ", name, 
                        "</br></br>x: ", x, 
                        "</br>y: ", y, 
                        "</br>coord: ", coord, 
                        "</br>cos2: ", cos2, 
                        "</br>contrib: ", contrib))
bggly

在 Stéphane Laurent 的帮助下。对于以第一列作为行名称的 .csv 格式的大型数据集，您可以将其读取为 df <- read.csv("Test_Data.csv", row.names = 1)，前提是您的行名称不重复。

在 PCA 图中命名样本

name the samples in a PCA plot

r

tooltip

pca

dataframe