I've read similar questions about that here, but still didn't work for my problem. I have a table with: columns with different kinds of pollutants levels and a column with the name of the samples. However, in no way I can change the name of the labels (now it's numbers) to the samples names.
Here is my script:
read.csv2("PCA_ALL.csv", header=TRUE)->tabela
tabela
pca <- prcomp(~Ter+Hop+UCM+AHS+S_Chain+L_chain+Alkyl+HMW+LMW+TOC, scale = TRUE)
fviz_pca_biplot(pca, geom = c("point","text"),
addEllipses = TRUE, ggtheme = theme_gray(),
col.var = "black", repel=FALSE,
title = "PCA - GB", xlab="PC1 (39%)", ylab="PC2 (22%)")
Does anyone know what I could do? Thanks in advance!
The first column of my table is named "area", where the name of the samples are.
Here is a possibile solution:
tabela <- read.table(text="
area Ter Hop UCM AHS S_Chain L_chain Alkyl HMW LMW TOC
1 2010-2004 0.71 3.10 119.4 136.8 0.10 3.48 11.50 7.70 16.70 1.19
2 2004-1999 0.57 2.77 71.0 89.3 0.04 2.61 3.74 3.61 1.30 0.81
3 1999-1993 0.87 3.10 117.7 132.1 0.04 2.77 6.38 3.08 1.94 0.90
4 1993-1988 0.49 2.69 98.4 111.7 0.04 2.64 4.60 3.57 1.81 0.86
5 1988-1982 1.44 4.43 80.0 93.9 0.05 3.10 7.27 3.84 2.92 1.06
6 1982-1977 0.57 4.80 55.1 65.5 0.03 3.80 9.87 5.50 8.80 1.25
7 1977-1971 0.62 3.16 174.7 190.8 0.04 3.15 6.00 3.58 1.51 1.08
8 1971-1966 1.17 5.77 162.3 174.8 0.04 3.39 5.95 5.68 2.65 1.11
9 1966-1960 1.28 8.13 155.4 194.6 0.05 5.61 5.74 5.47 2.45 1.16
10 1960-1954 0.69 6.77 96.0 134.2 0.04 5.51 3.74 4.73 2.41 1.16
11 1954-1949 0.75 4.56 65.8 122.6 0.07 4.91 7.97 5.33 2.48 0.83
12 1949-1943 0.58 4.74 70.2 112.3 0.05 5.38 4.94 7.47 3.19 1.19
13 1943-1938 3.00 6.22 66.9 105.9 0.08 5.78 16.20 8.40 3.79 1.19
14 1938-1932 0.77 3.44 96.4 141.7 0.06 4.93 8.48 3.60 4.12 1.06
15 1932-1927 0.40 4.37 84.7 126.3 0.04 4.36 3.73 3.67 1.66 0.90
16 1927-1921 1.95 5.06 51.8 92.5 0.07 5.08 11.74 4.36 5.29 1.01
", header=T)
pca <- prcomp(~Ter+Hop+UCM+AHS+S_Chain+L_chain+Alkyl+HMW+LMW+TOC, scale = TRUE, data=tabela)
# Set row names for the matrix with rotated data
dimnames(pca$x)[[1]] <- tabela$area
library(factoextra)
fviz_pca_biplot(pca, geom = c("point","text"),
addEllipses = TRUE, ggtheme = theme_gray(),
col.var = "black", repel=FALSE,
title = "PCA - GB", xlab="PC1 (39%)", ylab="PC2 (22%)")