In wdy91617/ggords: Ordination Visualization

knitr::opts_chunk$set(collapse = TRUE, comment = "#>", fig.width = 5, fig.height = 4.5, fig.align = "center")

library(ggords)
require(vegan)
require(ggplot2)
data(Envs)

get group factor

Env.w <- hclust(dist(scale(Envs)), "ward.D")
gr <- cutree(Env.w , k=4)
grl <- factor(gr)

Compute PCA

Env.pca <- rda(Envs,scale = TRUE)
#head(summary(Env.pca))

Produce a plot

ggpca(Env.pca)

Add a group

ggpca(Env.pca, group = grl) 

Set a theme

ggpca(Env.pca, group = grl, spacol = "white") + theme_dark()

Set a theme (use ggthemr packages, more themes in ggthemer)

# library(ggthemr)#https://github.com/cttobin/ggthemr
# chalk_theme <- ggthemr('chalk', set_theme = FALSE)  
# fd_theme <- ggthemr('flat dark', set_theme = FALSE)  
# p <- ggpca(Env.pca, group = grl, spacol = "white") 
# p + chalk_theme$theme
# p + fd_theme$theme

Remove the arrow

ggpca(Env.pca, group = grl, spearrow = NULL)

Modify legend title, group color and point shape

ggpca(Env.pca, group = grl, spearrow = NULL) + 
  scale_color_manual(name = "Groups",values = c("red2", "purple1", "grey20","cyan")) +
  scale_shape_manual(name = "Groups",values = c(8,15,16,17))

Add confidence ellipses

ggpca(Env.pca, group = grl, spearrow = NULL, ellipse = TRUE) +
  scale_colour_hue(l = 70, c = 300)

wdy91617/ggords documentation built on May 24, 2019, 2:47 p.m.