Description Usage Arguments Details Value Author(s) References See Also
Ordination plot
1 | vis_ordinate(data, type = "", transform = "", distmeasure = "", constrain = "")
|
obj |
(required) A data object of class 'ampvis2' (see amp_load) or class 'mmt' (see |
type |
(required) Type of ordination method. One of:
Note that PCoA is not performed by the vegan package, but the |
distmeasure |
(required for nMDS and PCoA) Distance measure used for the distance-based ordination methods (nMDS and PCoA). Choose one of the following:
You can also write your own math formula, see details in |
transform |
(recommended) Transforms the abundances before ordination, choose one of the following: |
filter_vars |
Remove low signal variables across all samples below this threshold in percent. Setting this to 0 may drastically increase computation time. (default: |
constrain |
(required for RDA and CCA) Variable(s) in the metadata for constrained analyses (RDA and CCA). Multiple variables can be provided by a vector, fx |
x_axis |
Which axis from the ordination results to plot as the first axis. Have a look at the |
y_axis |
Which axis from the ordination results to plot as the second axis. Have a look at the |
sample_color_by |
Color sample points by a variable in the metadata. |
sample_color_order |
Order the colors in |
sample_shape_by |
Shape sample points by a variable in the metadata. |
sample_colorframe |
Frame the sample points with a polygon by a variable in the metadata split by the variable defined by |
sample_colorframe_label |
Label by a variable in the metadata. |
sample_label_by |
Label sample points by a variable in the metadata. |
sample_label_size |
Sample labels text size. (default: |
sample_label_segment_color |
Sample labels repel-segment color. (default: |
sample_point_size |
Size of the sample points. (default: |
sample_trajectory |
Make a trajectory between sample points by a variable in the metadata. |
sample_trajectory_group |
Make a trajectory between sample points by the |
sample_plotly |
Enable interactive sample points so that they can be hovered to show additional information from the metadata. Provide a vector of the metadata variables to show, or |
var_plot |
(logical) Plot variable points or not. (default: |
var_nlabels |
Number of the most extreme variables labels to plot (ordered by the sum of the numerical values of the x,y coordinates. Only makes sense with PCA/RDA). |
var_label_by |
Label variable points by taxonomy ( |
var_label_size |
Size of the variables text labels. (default: |
var_label_color |
Color of the variables text labels. (default: |
var_rescale |
(logical) Rescale variables points or not. Basically they will be multiplied by 0.8, for visual convenience only. (default: |
var_point_size |
Size of the variables points. (default: |
var_shape |
The shape of the variables points, fx |
var_plotly |
(logical) Enable interactive variables points so that they can be hovered to show complete information. (default: |
envfit_factor |
A vector of categorical environmental variables from the metadata to fit onto the ordination plot. See details in |
envfit_numeric |
A vector of numerical environmental variables from the metadata to fit arrows onto the ordination plot. The lengths of the arrows are scaled by significance. See details in |
envfit_signif_level |
The significance threshold for displaying the results of |
envfit_textsize |
Size of the envfit text on the plot. (default: |
envfit_textcolor |
Color of the envfit text on the plot. (default: |
envfit_numeric_arrows_scale |
Scale the size of the numeric arrows. (default: |
envfit_arrowcolor |
Color of the envfit arrows on the plot. (default: |
envfit_show |
(logical) Show the results on the plot or not. (default: |
repel_labels |
(logical) Repel all labels to prevent cluttering of the plot. (default: |
opacity |
Opacity of all plotted points and sample_colorframe. |
detailed_output |
(logical) Return additional details or not (model, scores, inputmatrix, screeplot etc). If |
tax_empty |
(ampvis2 only) How to show OTUs without taxonomic information. One of the following:
|
... |
Pass additional arguments to the vegan ordination functions, fx the |
A wrapper around the vegan package to generate ggplot2 ordination plots suited for analysis and comparison of microbial communities. Simply choose an ordination type and a plot is returned.
The
function is primarily based on two packages; vis_ordinate
vegan-package
, which performs the actual ordination, and the ggplot2-package
to generate the plot. The function generates an ordination plot by the following process:
Various input argument checks and error messages
Filtering, where low abundant variables across all samples are removed (if not filter_vars = 0
is set)
Data transformation (if not transform = "none"
is set)
Calculate distance matrix based on the chosen distmeasure
if the chosen ordination method is PCoA/nMDS/DCA
Perform the actual ordination and calculate the axis scores for both samples and variables
Visualise the result with ggplot2 or plotly in various ways defined by the user
A ggplot2 object. If detailed_output = TRUE
a list with a ggplot2 object and additional data.
Kasper Skytte Andersen kasperskytteandersen@gmail.com
Thomas Yssing Michaelsen tym@bio.aau.dk
Mads Albertsen MadsAlbertsen85@gmail.com
GUide to STatistical Analysis in Microbial Ecology (GUSTA ME): https://mb3is.megx.net/gustame
Legendre, Pierre & Legendre, Louis (2012). Numerical Ecology. Elsevier Science. ISBN: 9780444538680
Legendre, P., & Gallagher, E. (2001). Ecologically meaningful transformations for ordination of species data. Oecologia, 129(2), 271-280. http://doi.org/10.1007/s004420100716
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