NMDS plotting issue
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12 months ago
arshad1292 ▴ 110


I have successfully generated the NMDS ordination (I think), and now want to plot it preferably using "ellipses". Here are all the script that I ran to reach to this step:

nmds <- read.csv(file = "mydata.csv", header = TRUE, row.names = 1) # read species data
nmds.env <- read.csv(file = "mydata_env.csv", header = T, row.names = 1) # read metadata or environment

And then

nmds1 <- metaMDS(nmds, distance = "bray", autotransform = FALSE)

This runs ordination and produces nice results (stress = 0.1)

Next, I run the following:

plot(nmds1) # this displays sites and species

All seems good until here. Next, when I try to plot it and use ellipses, then issue arises. Please see below:

ordiplot(nmds1, type = "n", main = "ellipses") # this runs fine
orditorp(nmds1, display = "sites", labels = F,  col = c("blue", "orange") [as.numeric(nmds.env$group)], cex = 1) # this produces error "NAs introduced by coercion" BTW I have only two groups that I want to colour blue and orange. 

As shown below, then I changed as.numeric to as.vector since I have a total of two groups and they are not numeric.

orditorp(nmds1, display = "sites", labels = F,  col = c("blue", "orange") [as.vector(nmds.env$group)], cex = 1)

The script runs but it produces no plot (no dots)

Next, when I run the following command:

ordiellipse(nmds1, groups = nmds.env$group, draw = "polygon", lty = 1, col = "grey90") # it draws empty ellipses nicely but contains no dots showing the data points. 

I want show the dots too. I have attached three figures.

  1. screenshot of "mydata.csv" file enter image description here
  2. screenshot of "mydata_env.csv" file enter image description here
  3. output of the plotting... that shows ellipses but no dots to represent data. enter image description here

Please help me in finding out where I went wrong with this. Thanks in advance!

NMDS metagenomic • 424 views

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