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fawda123 / ggord

a take on ordination plots using ggplot2
https://fawda123.github.io/ggord/
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Reducing number of vectors #14

Closed p-neves closed 5 years ago

p-neves commented 5 years ago

Hi:

Is it possible to reduce the number of plotted vectors on an ordination plot? I want to make an nmds plot and my vectors (species) are too many, obscuring the graph. Is there a way to define which vectors to plot, e.g. by setting a threshold on the abundance?

fawda123 commented 5 years ago

Here's a manual solution removing Sepal.Length using NA for vector type and label color:

ggord(ord, iris$Species, vectyp =  c(NA, 'solid', 'solid', 'solid'), labcol= c(NA, 'black', 'black', 'black'))

image

I think a bigger question though is whether or not its misleading to show some vectors and not others. If it's an issue of data overload, I would consider refitting the model with less species (or maybe group by genus?). Perhaps removing those with very low abundance would be a good start as rare species can really skew some multivariate methods.