PCA Biplot variable label customization

Question

I am trying to make PCA biplot by using follwoing code from the given data. In the data there are 4 type of genotypes, belongs to 4 type of species and 4 types of variables were evaluated (SPAD, PN, Y(II), DMC) under 2 type of conditions 1= control, 2=Stress. I successfully make the PCA biplot as shown in picture But I am havng trouble with variable labels shown alongwith the arrows. I want to convert the #1 and #2 into SUPERCRIPT CT and HS or I want to keep the original name for example "Y(II)" but in the grpah it always convert to "Y.II.". Also I want to change the color of the individual text as they are shown in Parameter legends and also keep the SPecies legend color to differentiate.

pca <- PCA(data.frame(data[,-2], row.names = 1), ncp=7, graph = TRUE, scale.unit = TRUE)

SPAD <- "Chlorophyll Index" 
IRGA <- "Gas exchange"
CF <- "Chlorophyll fluorescence"
ag <- "Morphological traits"
traits <- factor(c(SPAD,IRGA,CF,ag,SPAD, IRGA,CF,ag))

fviz_pca_biplot(pca, 
                geom.ind = c("point","text"),
                pointshape = 21,
                pointsize = 2.5,
                fill.ind = data$Species,
                col.ind = "black",
                col.var = traits,
                legend.title = list(fill = "Species", color = "Parameters"),
                repel = TRUE )+ 
  ggpubr::fill_palette("cosmic")+ # Indiviual fill color
  ggpubr::color_palette(c("brown", "purple", "red","blue")) +  # Variable colors
  theme_gray() + 
  theme(legend.position = "right", 
        legend.text = element_text(face="italic"),
        plot.caption = element_text(hjust = 0),
        legend.key.size = unit(0.5, 'cm'),
        legend.background = element_rect(fill='transparent'),
        panel.background = element_rect(colour = "grey30")) +
  labs(title = "", x= "PC1 (62.56%)", y= "PC2 (29.10%)", 
       caption = "*1: Control , 2: Heat stress")

Genotype	Species	SPAD1	Pn1	Y(II)1	DMC1	SPAD2	Pn2	Y(II)2	DMC2
BEL	sp1	0.6	14.38	0.25	0.21	1.64	16.5	0.29	-0.4
BGB003	sp2	-0.24	14.87	0.2	-1.24	-0.33	16.63	0.27	-1.24
BGB008	sp2	-0.54	11.92	0.14	-1.24	-0.37	12.6	0.15	-0.72
BGB083	sp3	-1.18	6.61	0.13	0.74	-0.04	5.41	0.16	0.63
BGB086	sp3	-0.89	9.05	0.19	-0.53	-0.33	11.2	0.17	-0.28
BGB088	sp4	-0.4	8.75	0.15	-0.39	0.28	12.36	0.22	-0.6
BGB089	sp4	-0.52	9.86	0.2	-0.05	0.47	11.06	0.19	-0.44

SamR · Accepted Answer · 2023-09-26 19:48:28Z

0

Your variables are stored in the row names of your pca object. You can edit them to get the plot you desire. In particular you can change e.g. DMC1 to DMC^1 and so on, to tell ggplot2 you want to use superscript:

pca$var <- lapply(pca$var, \(d) {
    # Replace Y.II. with Y(II)
    rownames(d) <- gsub("\\.II\\.", "(II)", rownames(d))
    # Replace e.g. DMC1 with DMC^1
    rownames(d) <- gsub("(1|2)$", "^\\1", rownames(d))
    d
})

When drawing your plot, make sure to add parse = TRUE, so it knows that DMC^1 should be treated as superscript.

fviz_pca_biplot(pca,
    geom.ind = c("point", "text"),
    pointshape = 21,
    pointsize = 2.5,
    fill.ind = data$Species,
    col.ind = "black",
    col.var = traits,
    legend.title = list(fill = "Species", color = "Parameters"),
    repel = TRUE,
    parse = TRUE # this is important
) # + all your theme code goes here

Output:

answered Sep 26, 2023 at 19:48

SamR

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2 Comments

Ikram Bashir Over a year ago

Thanks for the answer @SamR . I have one more question, what if I need to add Symbol instead of "Y" such as phi, Sigma or anyother greek symbol??

SamR Over a year ago

With relatively recently versions of R you should just be able to enter "φ", "σ", etc. directly in the code

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