Ploting負荷PCA VS波數

Question

我有矩陣數據

Wavenumber 450.000000 451.00000 
Sample 1.977876 1.977388 1.976533 
Sample2 1.803184 1.802537 1.802181 ... 
... 
Sample29 1.929462 1.928509 1.927309 

我除去與下面的命令的第一行只與樣品來繪製圖形，讀取文件的csv後。

s<- as.data.frame(t, nrow.names =1) 
s.pca <- prcomp(s[-c(1),], center = TRUE, scale. = TRUE) 
sd <- s.pca$sdev 
loadings <- s.pca$rotation 
rownames(loadings) <- colnames(s) 
scores <- s.pca$x 
library(ggplot2) 
scores=as.data.frame(s.pca$x) 
###---Plot Components PC1 and PC2 
p<- ggplot(data = scores, obs.scale = .8, var.scale = 1, show.names=TRUE, aes(x = PC1, y = PC2, label = rownames(scores))) 
p<- p + geom_hline(yintercept = 0, colour = "gray65") 
p<- p + geom_vline(xintercept = 0, colour = "gray65") 
p<- p + geom_text(colour = "black", alpha = 0.8, size = 4) 
p<- p + ggtitle("PCA plot Samples") 
p<- p + theme(axis.title = element_text(family = "Arial", color="#666666", face="bold", size=16)) 
p<- p + theme(axis.text.x = element_text(face="bold", color="#993333", size=14,angle=0)) 
p<- p + theme(axis.text.y = element_text(face="bold", color="#993333", size=14, angle=0)) 
p<- p + xlab("PC1") 
p<- p + ylab("PC2") 
print(p) 

我刪除了第一線，我不知道我怎樣才能使一個負載（PC1和PC2）與基體的波數？

Answer 1

由於我們沒有您的數據，下面是一個使用chemometrics數據包的簡單示例。它是分類數據，但您可以擴展該示例以將波數用作x座標。

library("ggplot2") 
library("chemometrics") 
data(glass) 
glass.pca <- prcomp(glass) 
loadings <- as.data.frame(glass.pca$rotation) 
# add in the element info: 
loadings <- data.frame(element = colnames(glass), loadings) 
qplot(x = element, y = PC1, data = loadings, main = "Loadings for PC1", xlab = "Compound/Element") 

或者，如果你想要的分數：

scores <- as.data.frame(glass.pca$x) 
qplot(x = PC1, y = PC2, data = scores, main = "Score Plot") 

編輯：使用你的數據（不是在一個方便的形式，你應該學會使用hyperSpec或ChemoSpec）

Wave <- read.csv("matrix.csv", nrows = 1) 
Int <- read.csv("matrix.csv", skip = 1) 
SampNames <- Int[,1] 
Int <- Int[,-1] 
Fabio <- prcomp(Int) 

scores <- Fabio$x 
rownames(scores) <- SampNames 
scores <- as.data.frame(scores) 
qplot(x = PC1, y = PC2, data = scores, geom = "point") 

loadings <- Fabio$rotation 
rownames(loadings) <- Wave 
loadings <- cbind(wave = unlist(Wave), loadings) 
loadings <- as.data.frame(loadings) 
qplot(x = wave, y = PC1, data = loadings, geom = "line")