User Tools

Site Tools


en:ordiagrams_rscript
# Plotting ordination diagrams (ordination diagrams - theory)
 
png ('ordiplots_dune.png', width = 8, height = 8, units = 'in', pointsize = 11, res = 300)
par (mfrow = c(2,2))
 
PCA <- rda (spe)
biplot (PCA, scaling = 2, main = 'PCA')
 
 
CA <- cca (spe)
plot (CA, main = 'CA', scaling = 2)
 
 
RDA <- rda (spe ~ Moisture + Management, env)
#anova (RDA, by = 'margin')
plot_RDA <- plot (RDA, scaling = 2, main = 'RDA', type = 'n')
text (plot_RDA, what = 'sp', arrow = T, length = 0.05, col='red', cex=0.7)
text (plot_RDA, what = 'si', cex = 0.7)
text (plot_RDA, what = 'centroids', col = 'blue')
text (plot_RDA, what = 'biplot', arrow = TRUE, length = 0.05, col = 'blue', xpd = TRUE)
 
CCA <- cca (spe ~ Moisture + Management, env)
#anova (CCA, by = 'margin')
plot_CCA <- plot (CCA, scaling = 2, main = 'CCA', type = 'n')
text (plot_CCA, what = 'sp', col='red', cex=0.7)
text (plot_CCA, what = 'si', cex = 0.7)
text (plot_CCA, what = 'centroids', col = 'blue')
text (plot_CCA, what = 'biplot', arrow = TRUE, length = 0.05, col = 'blue', xpd = TRUE)
 
dev.off ()
 
png ('ordiplots_types.png', width = 8, height = 8/3, units = 'in', pointsize = 14, res = 300)
par (mfrow = c(1,3))
ordiplot (CCA, display = 'si', ann = F, axes = F)
box ()
title (main = 'Scatterplot', sub = '(o = sample scores)')
 
ordiplot (CCA, display = c('si', 'sp'), ann = F, axes = F)
box ()
title (main = 'Biplot', sub = '(o = sample, + = species scores)')
 
plot_CCA <- plot (CCA, type = 'n', ann = F, axes = F)
box ()
points (CCA, display = 'sp', col = 'red', cex = 0.6, pch = '+')
points (CCA, display = 'si', cex = 0.6)
text (plot_CCA, what = 'centroids', col = 'blue', labels = rep ('X', 4), cex = 0.6)
text (plot_CCA, what = 'biplot', arrow = TRUE, length = 0.05, col = 'blue', xpd = TRUE, labels = '')
 
title (main = 'Triplot', sub = '(o = sample, + = species scores,\nvector & centroid = env. vars)')
box ()
dev.off ()
en/ordiagrams_rscript.txt · Last modified: 2019/02/05 21:50 by David Zelený