How to plot the factors (spp) of the metaMDS result using ggplot2, related to the collection sites in the original data frame?

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Given the following data frame:

dat<-data.frame(
  "sitio" = c("a", "a", "a",'a', "b", "b", "b", 'b', "c", "c", "c",'c'),
  "amostra"=c(rep(1,4),rep(2,4),rep(3,4)),
  "sp1"=c(1,3,3,2,4,2,1,5,3,6,1,5),
  "sp2"=c(1,3,3,2,4,2,1,5,3,6,1,5),
  "sp3"=c(1,3,3,2,4,2,1,5,3,6,1,5),
  "sp4"=c(2,3,4,1,5,3,1,5,5,8,9,1),
  "sp5"=c(3,4,3,1,6,7,5,8,3,1,3,2)
)

I want to see the grouping of the species according to the collection site, filling the result of the metaMDS, using ggplot2.

library(vegan)
library(ggplot2)
dmds<-metaMDS(dat[,3:7], distance = "bray", autotransform = FALSE)
mds1 <- dmds$points[,1]
mds2 <- dmds$points[,2]
plt<-cbind(dat,mds1,mds2)
spp<-dmds$species
ggplot(plt,aes(mds1,mds2, shape=sitio,color=sitio))+
  geom_point()+
  geom_text(aes(label=spp))

I tried using geom_text, labeling the MDS species, but as it has a different number of lines, it gives the following error.

Error: Aesthetics must be either length 1 or the same as the data (12): label

How could you join the MDS result with the original data frame to access the species and the sites, being able to visualize everything in a graph?

[Seria algo assim, mas com os nomes das espécies]

Following the example given by @Imonferrari, the graph looks like this.

Gráfico final seguindo o exemplo de Imonferrari

r ggplot2

  • What would your final chart look like? You want to post sp1/sp2... on the strings of mds1 and mds2 in spp?

  • I want species names to appear at the same points as 'a', 'b' and 'c'.

  • that last Plot is the result you expect or the result you are generating?

  • That’s what I hope, it’s just an example, I did using geom_text(aes(label="spp")).

  • Right, but look at the species would be sp1, sp2 right? I can help you with ggplot but I don’t know the type of data, so I’d like to understand more of how you want the final graph

  • In case you want to plot the points of dmds$Species? ggplot(data=plt, aes(mds1, mds2)) +&#xA; geom_point(aes(shape = sitio, color = sitio)) +&#xA; geom_text(data = spp, aes(MDS1, MDS2, label = especies)) Like this?

  • This plots the spp related to each 'place'. I circled your example, but it gives the same error.Error: Aesthetics must be either length 1 or the same as the data (5): x and y

  • opa, before making the graph turn spp['especies'] <- rownames(spp), q creates a column with the name of the species. This part was missing

  • @Jorgemendes gives error too, because of MDS1 and MDS2 are 5 lines each and the df total is 12.

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1 answer

1


You can pivot:

library(tidyr)
library(dplyr)

teste <- plt %>% pivot_longer(
  cols = starts_with('sp'),
  names_to = 'species',
  values_to = 'values'
)

And then plot:

ggplot(teste, aes(mds1, mds2, shape = sitio, color = sitio))+
  geom_point()+
  geom_text(label = teste$species)

  • Yeah, I thought of something like this, put all the spp in one column, but I couldn’t find the way. Now, what do I do because in my data frame all species start with different letters and I have 55.

  • Do the columns follow an order? If they follow you can slicing, where is it colswithin the pivot_longer you would put something: cols = colnames(plt)[3:7] in this our sample date.frame will return : '"sp1" "sp2" "sp3" "sp4" "sp5"'.

  • This example answers your question?

  • Answer yes, thank you. I checked with your example in the original df, but the chart doesn’t look good. I’ll put it so you can see it.

  • Is there a way to make available the dataset you are using in full? What do you want to improve in the chart?

  • I can’t. I marked your answer as the best solution, it really helped. It turns out that when you put all the spp in one column, all the spp labels are on top of each other.

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