gghpcc

install

if(!require(ggcorrr))
  devtools::install_github("houyunhuang/ggcorrr")
devtools::install_github("houyunhuang/gghpcc")

examples

library(ggcorrr)
library(gghpcc)
library(dplyr)
library(vegan)
data(varespec)
data(varechem)
## group by rows
spec_df <- varespec %>% 
  mutate(grp = rep(LETTERS[1:3], 8))

env_df <- varechem %>% 
  mutate(grp = rep(LETTERS[1:3], 8))

df_grp <- fortify_mantel(spec_df, env_df, 
               spec_group = "grp",
               env_group = "grp",
               mantel_fun = "mantel",
               pair_test = TRUE,
               env_corr_params = list(type = "upper", 
                                      show_diag = FALSE,
                                      corr_test = TRUE, 
                                      cluster = TRUE))
ggmantel(df_grp)

four group

df4 <- fortify_mantel(varespec, varechem, 
                     spec_select = list(spec01 = 22:25, 
                                        spec02 = 1:4, 
                                        spec03 = 38:43, 
                                        spec04 = 15:20),
                     mantel_fun = "mantel",
                     env_corr_params = list(type = "upper", 
                                            show_diag = FALSE,
                                            corr_test = TRUE, 
                                            cluster = TRUE))
ggmantel(df4) 

three group

df3 <- fortify_mantel(varespec, varechem, 
                      spec_select = list(spec01 = 22:25, 
                                         spec02 = 1:4, 
                                         spec03 = 38:43),
                      mantel_fun = "mantel",
                      env_corr_params = list(type = "upper", 
                                             show_diag = FALSE,
                                             corr_test = TRUE, 
                                             cluster = TRUE))
ggmantel(df3)

two group

df2 <- fortify_mantel(varespec, varechem, 
                      spec_select = list(spec01 = 22:25, 
                                         spec02 = 1:4),
                      mantel_fun = "mantel",
                      env_corr_params = list(type = "upper", 
                                             show_diag = FALSE,
                                             corr_test = TRUE, 
                                             cluster = TRUE),
                      get_link_params = list())
ggmantel(df2)

1 group

df1 <- fortify_mantel(varespec, varechem, 
                      spec_select = list(spec01 = 22:25),
                      mantel_fun = "mantel",
                      env_corr_params = list(type = "lower", 
                                             show_diag = FALSE,
                                             corr_test = TRUE, 
                                             cluster = TRUE))
ggmantel(df1, curvature = 0.05)