R中的主成分分析，ggbiplot答案

【问题标题】：Principal Component Analysis in R, ggbiplotR中的主成分分析，ggbiplot
【发布时间】：2016-06-10 13:03:00
【问题描述】：

我是一名尝试使用 R 的生物学家，但我正在努力解决它。

我正在尝试为此数据生成主成分分析：

1,26.96,37.31,35.74
1,24.27,38.48,37.24
1,23.58,35.64,40.78
1,24.29,35.72,39.99
1,26.43,37.72,35.85
1,28.80,46.96,24.24
2,30.05,44.86,25.09
2,26.59,47.24,26.17
2,30.55,45.70,23.75
2,25.95,48.77,25.28
2,23.31,50.11,26.59
2,31.29,43.88,24.82
3,14.70,37.65,47.65
3,17.11,36.14,46.75
3,15.83,36.83,47.34
3,13.77,38.39,47.84
3,17.76,35.02,47.22
3,12.90,38.29,48.81

第一列对应group变量，我有3个组。

我看到HERE，如何制作我想要的图表。但是每次我到达生成双图部分时，我都会收到消息：

错误：提供给离散刻度的连续值。

这是我正在使用的代码：

>data(GPA2)
>head(GPA2, 3) 
>log.ir <- log(GPA2[, 2:4])
>ir.group <- GPA2[, 1]
>ir.pca <- prcomp(log.ir,center = TRUE,scale = TRUE) 
>print(ir.pca)
>plot(ir.pca, type = "l")
>summary(ir.pca)
>predict(ir.pca, newdata=tail(log.ir, 2))
>g <- ggbiplot(ir.pca, obs.scale = 1, var.scale = 1, groups = ir.group, ellipse = TRUE, circle = TRUE)
>g <- g + scale_color_discrete(name = '')
>g <- g + theme(legend.direction = 'horizontal', legend.position = 'top')
>print(g)

谁能帮帮我？

【问题讨论】：

标签： r pca ggbiplot

【解决方案1】：

您的分组变量必须是一个非数字因素

library(ggbiplot)
GPA2 <- data.frame(
  ir.group = sample(c(1,2,3),10, replace = TRUE),
  x = sample(1:10),
  y = sample(1:10),
  z = sample(1:10)
)

data(GPA2)
head(GPA2, 3) 
log.ir <- log(GPA2[, 2:4])
ir.group <- GPA2[, 1]
ir.pca <- prcomp(log.ir,center = TRUE,scale = TRUE) 
print(ir.pca)
plot(ir.pca, type = "l")
summary(ir.pca)
predict(ir.pca, newdata=tail(log.ir, 2))
g <- ggbiplot(ir.pca, obs.scale = 1, var.scale = 1, groups = as.factor(ir.group), ellipse = TRUE, circle = TRUE)
g <- g + scale_color_discrete(name = '')
g <- g + theme(legend.direction = 'horizontal', legend.position = 'top')
print(g)

【讨论】：

【解决方案2】：

您在第一列中的分组变量是一个整数 (1,2,3)，它必须是一个字符串，将其替换为“group 1”、“group 2”、“group 3”之类的内容（不带“”）。然后，您的数据将如下所示：

group 1,26.96,37.31,35.74
group 1,24.27,38.48,37.24
group 1,23.58,35.64,40.78
group 1,24.29,35.72,39.99
group 1,26.43,37.72,35.85
group 1,28.80,46.96,24.24
group 1,30.05,44.86,25.09
group 2,26.59,47.24,26.17
group 2,30.55,45.70,23.75
group 2,25.95,48.77,25.28
group 2,23.31,50.11,26.59
group 2,31.29,43.88,24.82
group 3,14.70,37.65,47.65
group 3,17.11,36.14,46.75
group 3,15.83,36.83,47.34
group 3,13.77,38.39,47.84
group 3,17.76,35.02,47.22
group 3,12.90,38.29,48.81

【讨论】：