Description Usage Arguments Value Examples
Generate NMDS points, group centroids and standard error ellipses
1 2 3 4 5 6 7 8 9 10 11 | NMDS_ellipse(
metadata,
OTU_table,
grouping_set,
distance_method = "bray",
rand_seed = 77777,
MDS_trymax = 1000,
autotransform = FALSE,
wascores = TRUE,
expand = FALSE
)
|
metadata |
A dataframe containing the metadata relating to the samples in your OTU table. Seems to break if this dataframe only has 1 column. |
OTU_table |
an OTU table with samples as rows and taxa as columns |
grouping_set |
a column name from your metadata. This column should contain information about how your samples should be grouped for centroid and ellipse calculation |
distance_method |
a single text value that describes the desired distance metric to use, must be accepted by the function vegdist() |
rand_seed |
numeric value to use as a random seed (for reproducability?) |
MDS_trymax |
number of iterations to use for the metaMDS call, default is 1000 |
autotransform |
passed to vegan's metaMDS, should community data be transformed? Should be TRUE/FALSE. Default = FALSE |
wascores |
passed to vegan's metaMDS, should species scores be calculated? Should be TRUE/FALSE. Default = TRUE |
expand |
passed to vegan's metaMDS, should species scores be expanded? |
Returns a list containing 3 items. [[1]] = input metadata with NMDS coordinates, group centroid coordinates for each sample. [[2]] = a dataframe containing information about the standard error confidence ellipses for each group. This datafame contains 100 points per group and is suitable for using with geom_path(). [[3]] = the ordination object created by the vegan function metaMDS().
1 | #soon
|
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