Hello,
I would like to perform an rda by having my sampleID sites colored according to their cluster membership (Clust).
I made this code but unable to do it
Clust <- tibble::tribble(
~SampleID, ~cluster,
"1A", 1
"1C", 1
"1D", 1
"1E", 2
"1F", 3
"1G", 3
"1H", 2
"2A", 2
"2B", 1
"2C", 1
"2D", 3
"2E", 3
"2F", 2
"2H", 1
)
Env <-tibble::tribble(
~SampleID, ~Dissolved.oxygen, ~pH, ~WT, ~Turbidity, ~ORP, ~Ammonium, ~Nitrates, ~BGA, ~Chlrophyll, ~CE, ~AT, ~Evaporation, ~Precipitation,
"1A", 4.24, 9.94, 24.48, 87.3, 97, 4.46, 3.6, 279133, 36.6, 1.074, 13.95, 4.34, 2.55,
"1C", 2.85, 9.98, 24.01, 98.8, 102.9, 4.37, 3.57, 265304, 40, 1.081, 13.95, 4.34, 2.55,
"1D", 3.81, 9.07, 26.67, 24.9, 94, 5.6, 3.53, 11603, 44, 1.147, 17.11, 5.8, 4.54,
"1E", 2.64, 8.99, 24.01, 43.1, 63.9, 3.38, 2.55, 218471, 35, 1.156, 17.11, 5.8, 4.54,
"1F", 4.61, 8.93, 23.5, 49.1, 64.7, 3.21, 2.28, 226658, 32.8, 1.157, 17.11, 5.8, 4.54,
"1G", 5.74, 9.24, 24.46, 68.6, 40.3, 1.93, 0.71, 267389, 44, 1.072, 17.9, 6.86, 6.88,
"1H", 3.69, 9.32, 24.65, 69.8, 48.1, 2.21, 1.2, 267144, 44.8, 1.152, 17.9, 6.86, 6.88,
"2A", 4.24, 9.94, 24.48, 87.3, 97, 4.46, 3.6, 279133, 36.6, 1.074, 13.95, 4.34, 2.55,
"2B", 2.66, 10, 24.92, 113, 111.9, 4.75, 3.21, 270193, 39.8, 1.081, 13.95, 4.34, 2.55,
"2C", 2.85, 9.98, 24.01, 98.8, 102.9, 4.37, 3.57, 265304, 40, 1.081, 13.95, 4.34, 2.55,
"2D", 3.81, 9.07, 26.67, 24.9, 94, 5.6, 3.53, 11603, 44, 1.147, 17.11, 5.8, 4.54,
"2E", 2.64, 8.99, 24.01, 43.1, 63.9, 3.38, 2.55, 218471, 35, 1.156, 17.11, 5.8, 4.54,
"2F", 4.61, 8.93, 23.5, 49.1, 64.7, 3.21, 2.28, 226658, 32.8, 1.157, 17.11, 5.8, 4.54,
"2H", 3.69, 9.32, 24.65, 69.8, 48.1, 2.21, 1.2, 267144, 44.8, 1.152, 17.9, 6.86, 6.88
)
Spe <-tibble::tribble(
~SampleID, ~Cyanobacteriaceae, ~Microcystaceae, ~Nostocaceae,
"1A", 1.342953283, 0, 0,
"1C", 1.966304234, 0, 0,
"1D", 0, 0, 1.80374141,
"1E", 1.492119211, 0, 1.492119211,
"1F", 0.597623166, 0, 0,
"1G", 1.319782597, 0, 0,
"1H", 0.859080227, 6.52598632, 0.859080227,
"2A", 0, 0, 1.907218755,
"2B", 0.793958833, 0, 0,
"2C", 0, 2.023336602, 0,
"2D", 0.859080227, 0, 0,
"2E", 0, 0, 2.333056481,
"2F", 0, 4.129704923, 0,
"2H", 0, 0, 2.333056481,
clust$cluster <- as.character(clust$cluster)
levels(clust$cluster) <- c("Area1","Area2","Area3"))
bg <- c("blue","green","red")
eco <- clust$cluster
rda_object <- rda(Spe[,-1], Env, scale=TRUE)
# axes 1 & 2
plot(spe.rda, type="n", scaling=1)
text(spe.rda, display="species", pch=20, cex=1, col="red", scaling=1)
points(spe.rda, display="sites", pch=20, cex=1.3, scaling = 1, bg=bg[eco])
text(spe.rda, scaling=1, display="bp", col="darkorange", cex=1)