Issue with RDA plot in R - r

Question

I am a novice in using R for multivariate analysis . I am trying to get a RDA plot depicting the relationship between my species abundance and environmental data. I have 6 environmental variables. But when I obtain the plot, I am able to see only only two vectors representing two variables alone. The commands I have used are below.
data <- read.csv("all_data.csv",h=T);
library(vegan)
sp1 <- data[,c("Sample","Acidobacteria","Actinobacteria","Aquificae","Bacteroidetes")];
env1 <- data[,c("Nitrogen","TOC","Phosphate","Sand","Silt","Clay")];
myrda <- rda(sp1,env1)
plot(myrda,scaling=2)
Someone please help me out with this. I wish to see all the 6 environmental parameters in my RDA plot.

Answer 1

Here is an example using vegan's example data varespec and varechem. The plot of the rda model automatically displays all 14 environmental variables:
library(vegan)
data(varespec)
data(varechem)
myrda <- rda(varespec, varechem)
myrda
colnames(varechem) # 14 variables
plot(myrda,scaling=2) # 14 vectors shown
Maybe double check that your data.frames correctly contain variable names so thet the plot knows where to grab labels. I would also make sure that your data splitting is working correctly - I don't think that your method will always work. Here is a possible alternative that should:
sp.incl <- match(c("Sample","Acidobacteria","Actinobacteria","Aquificae","Bacteroidetes"), colnames(data))
sp1 <- data[,sp.incl]
env.incl <- match(c("Nitrogen","TOC","Phosphate","Sand","Silt","Clay"), colnames(data))
env1 <- data[,env.incl]