Statistical Analysis of Microbiome Data with R by Yinglin Xia & Jun Sun & Ding-Geng Chen
Author:Yinglin Xia & Jun Sun & Ding-Geng Chen
Language: eng
Format: epub
ISBN: 9789811315343
Publisher: Springer Singapore
Finally, the function stressplot() is used to draw the Shepards stress plot. The function stressplot() generates two figures: one plots ordination distances versus observed dissimilarity (the chosen community dissimilarities), along with a monotone step line to show the fit; another plots goodness of fit to assess goodness of ordination of NMDS2 versus NMDS1 of particular samples. The following R codes are used to divide plotting window into two panels:
> par (mfrow = c(1,2))
The function plot() draws NMDS ordination diagram with sites (samples):
> stressplot (bc_nmds)
> plot (bc_nmds, display = 'sites', type = 't', main = 'Goodness of fit')
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