vis_ordinate.RdOrdination plot
vis_ordinate(data, type = "", transform = "", distmeasure = "", constrain = "")
| obj | (required) A data object of class 'ampvis2' (see amp_load) or class 'mmt' (see |
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| 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 ggplot2 object. If detailed_output = TRUE a list with a ggplot2 object and additional data.
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 vis_ordinatevegan-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
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