Correlation Plot

Create a correlation plot from a metacoder/taxmap object.

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

Arguments

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".

Value

A 1:1 correlation plot built with ggplot2.

Details

Correlation plots help to better explain the heat tree findings.

See also

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

Examples

# 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")
 }
# }