clockrate_reg_plot: Plot regression lines between sets of rates

In EvoPhylo: Pre- And Postprocessing of Morphological Data from Relaxed Clock Bayesian Phylogenetics

Plot regression lines between sets of rates

Description

Displays a scatterplot and fits regression line of one set of clock rates against another, optionally displaying their Pearson correlation coefficient (r) and R-squared values (R^2).

Usage

clockrate_reg_plot(rate_table, clock_x, clock_y,
                   method = "lm", show_lm = TRUE,
                   ...)

Arguments

rate_table	A table of clock rates, such as from the output of get_clockrate_table_MrBayes.
clock_x, clock_y	The clock rates that should go on the x- and y-axes, respectively.
method	The method (function) used fit the regression of one clock on the other. Check the method argument in the to geom_smooth function of ggplot2 for all options. Default is "lm" for a linear regression model. "glm" and "loess" are alternative options.
show_lm	Whether to display the Pearson correlation coefficient (r) and R-squared values (R^2) between two sets of clock rates.
...	Other arguments passed to geom_smooth.

Details

clockrate_reg_plot() can only be used when multiple clocks are present in the clock rate table. Unlike clockrate_summary and clockrate_dens_plot, no "clade" column is required.

Value

A ggplot object, which can be modified using ggplot2 functions.

See Also

vignette("rates-selection") for the use of this function as part of an analysis pipeline.

geom_point, geom_smooth

Examples

# See vignette("rates-selection") for how to use this
# function as part of an analysis pipeline

data("RateTable_Means_3p_Clades")

#Plot correlations between clocks 1 and 3
clockrate_reg_plot(RateTable_Means_3p_Clades,
                   clock_x = 1, clock_y = 3)

#Use arguments supplied to geom_smooth():
clockrate_reg_plot(RateTable_Means_3p_Clades,
                   clock_x = 1, clock_y = 3,
                   color = "red", se = FALSE)

EvoPhylo documentation built on Nov. 4, 2022, 1:06 a.m.