correlation_plot: Correlation Plot
In vallenderlab/MicrobiomeR: Analyze Microbiome Data

Description Usage Arguments Details Value See Also Examples

Create a correlation plot from a metacoder/taxmap object.

1 2	correlation_plot(obj, primary_rank, secondary_rank = TRUE, wp_value = 0.05, pal_func = NULL, trans = "logit")

`obj`	An object to be converted to a Taxmap object with `create_taxmap`.
`primary_rank`	The primary rank used to label the points.
`secondary_rank`	The secondary rank used to color the points. Can be an integer specifying the number of supertaxon ranks above the primary rank or the name of a supertaxon rank. Default: TRUE
`wp_value`	The Wilcoxian P-Value used to represent significant points. Default: 0.05
`pal_func`	A palette function that returns grDevices::colorRampPalette.
`trans`	Either the name of a transformation object, or the object itself given to `scale_continuous`. Built-in transformations include "asn", "atanh", "boxcox", "exp", "identity", "log", "log10", "log1p", "log2", "logit", "probability", "probit", "reciprocal", "reverse" and "sqrt".

Correlation plots help to better explain the heat tree findings.

A 1:1 correlation plot built with ggplot2.

create_taxmap, validate_MicrobiomeR_format, correlation_data, plot_limits, get_color_palette

ggplot, aes, geom_polygon, geom_point, labs, scale_continuous, scale_manual, guide_legend, geom_abline

geom_label_repel

fct_reorder

Other Visualizations: alpha_diversity_plot, correlation_data, correlation_plots, heat_tree_parameters, heat_tree_plots, ordination_plots, ordination_plot, plot_limits, save_alpha_diversity_plots, save_correlation_plots, save_heat_tree_plots, save_ordination_plots, save_stacked_barplots, stacked_barplots, stacked_barplot, top_coefficients_barplot

## Not run: 
if(interactive()){
# This example uses data that are no longer available in the MicrobiomeR package,
# however, they can be easily generated with \code{\link{MicrobiomeR}{as_analyzed_format}}.
library(MicrobiomeR)
analyzed_silva <- as_MicrobiomeR_format(MicrobiomeR::raw_silva_2, "analyzed_format")
correlation_plot(analyzed_silva, primary_rank = "Class", secondary_rank = "Phylum")
 }

## End(Not run)