I don't want that smaller, inner, deeper coloured points in the geom point in the graph. How do I get rid of it? I tried playing around with shapes but nothing happened.
library(stats)
library(ggfortify)
sp1 <- rnorm(72, mean = 4, 1)
sp2 <- rnorm(72, mean = 2, 1)
sp3 <- rnorm(72, mean = 3, 1)
sp4 <- rnorm(72, mean = 9, 1)
temp <- rnorm(72, mean = 20, 5)
season <- rep(c("Summer", "Autumn","Winter", "Spring"), each = 18)
sp.abd <- data.frame(sp1, sp2, sp3, sp4, season, temp)
pca_res <- prcomp(sp.abd[,-c(5,6)], scale. = TRUE)
autoplot(pca_res,
loadings = TRUE, loadings.colour = 'blue',
loadings.label = TRUE, loadings.label.size = 3) +
theme_classic() + geom_point(aes(color = sp.abd$season), size = 6, alpha = 0.5) +
scale_color_manual(values = rainbow(12,s = 0.6, start = 0, end = 0.7, rev = TRUE))
Following Randy's answer below I try to replicate it for colouring by temp (a gradient here)
autoplot(pca_res, sp.abd, color = temp,
loadings = TRUE, loadings.colour = 'blue',
loadings.label = TRUE, loadings.label.size = 3) +
scale_colour_gradient2(low = "white", mid = "cyan", high = "dodgerblue4", na.value = NA)
It generates just a gray plot. Only if I call colour outside the autoplot command does it use the scale_colour_gradient2 option. But this is still with the dots
autoplot(pca_res, size = 6, alpha. = 0.5,
loadings = TRUE, loadings.colour = 'blue',
loadings.label = TRUE, loadings.label.size = 3) + geom_point(aes(colour = sp.abd$temp)) +
scale_colour_gradient2(low = "white", mid = "cyan", high = "dodgerblue4", na.value = NA)
It looks like autoplot.prcomp
(the autoplot
method for prcomp
objects as specified by ggfortify
) already handles making the points without a geom_point()
call, so you can put the color mapping, point size, and point opacity inside autoplot
:
library(stats)
library(ggfortify)
sp1 <- rnorm(72, mean = 4, 1)
sp2 <- rnorm(72, mean = 2, 1)
sp3 <- rnorm(72, mean = 3, 1)
sp4 <- rnorm(72, mean = 9, 1)
season <- rep(c("Summer", "Autumn","Winter", "Spring"), each = 18)
sp.abd <- data.frame(sp1, sp2, sp3, sp4, season)
pca_res <- prcomp(sp.abd[,-5], scale. = TRUE)
autoplot(pca_res,
################
# Add this stuff
data = sp.abd,
color = 'season',
size=6, alpha=.5,
################
loadings = TRUE, loadings.colour = 'blue',
loadings.label = TRUE, loadings.label.size = 3) +
theme_classic() +
scale_color_manual(values = rainbow(12,s = 0.6, start = 0, end = 0.7, rev = TRUE))