otuSummary (version 0.1.1)

ordination: Quickly check the constrained or unconstrained ordination plot

Description

This is a wrapped function to quickly generate a diagnostic ordination plot. It can visualize the rda and cca, either in constrained or unconstrained, as well as the NMDs.

Usage

ordination(otutab, env=NULL, SiteInRow=TRUE, percent=TRUE, mySite=NULL, ordtype ="urda",
    scale = TRUE, display = "sites", choices = 1:2, biplot = FALSE,
    legPos = "bottomright", showsite = FALSE, saveplot = FALSE, ...)

Arguments

otutab

A OTU table of microbial community, without a taxonomy column.

env

Optional, a environmental table, which should contains the same samples as the OTU table. If given, a constrained ordination will be processed. If env is NULL as default, the ordination will be unconstrained.

SiteInRow

Logical, if "TRUE", the OTU table contains samples in rows and taxa in columns, as this function is dependent on several vegan functions and thus follows its data format. The function will transpose the otu table if "SiteInRow" is FALSE.

percent

Logical, specify whether the input otu table are in relative abundance.

mySite

Factor, specify the sample grouping in the ordination plot, which is NULL by default.

ordtype

Character, specify the type of ordination, the valid choice are c("urda", "ucca", "unmds") for unconstrained ordination, and c("c_rda", "c_cca", "c_nmds") for constrained ones.

scale

Logical, whether scale species to unit variance (like correlations).

display

Character, to access scores for "sites" or "species".

choices

Numeric, vector of length two. Specify which axes to be shown, e.g. choices = 1:2, choices = c(1,3).

biplot

Logical, draws a biplot with species scores indicated by biplot arrows, only works in unconstrained ordination.

legPos

Character, the position of the legend in the plot. The valid choices are c("topleft", "topright", "bottomleft" and "bottomright")

showsite

Logical, whether show the site labels in the ordination.

saveplot

Logical, whether the ordination plot will be saved to the default work directory.

...

arguments, including graphical parameters of ordination object in vegan, passed to other methods.

Author

Sizhong Yang <[e-mail]>

Details

The function wrapped several functions in 'vegan' package to quickly have a diagnostic ordination for your data. For better performance and more custom controls on plotting, please use the corresponding functions in the package 'vegan' (Oksanen et al, 2013).

References

Oksanen J, Blanchet FG, Kindt R, Legendre P, Minchin PR, O'Hara RB et al (2013). vegan: Community Ecology Package. R package version 2.0-7. http://CRAN.R-project.org/package=vegan.

See Also

The vegan manual at https://cran.r-project.org/web/packages/vegan/index.html

Examples

data(varespec)
data(varechem)

ordination(otutab = varespec, env = NULL, SiteInRow = TRUE, percent = FALSE,
    mySite = NULL, ordtype = "urda", display = "sites", biplot = FALSE,
    legPos = "bottomright", showsite = FALSE, saveplot = FALSE)

ordination(otutab = varespec, env = varechem, SiteInRow = TRUE, percent = FALSE,
    mySite = NULL, ordtype = "c_rda", display = "sites", biplot = FALSE,
    legPos = "bottomright", showsite = FALSE, scale = TRUE)