programs/4_displays/41_plot_ri_results.R

In bsaul/elktoeChemistry: Data and code for Elktoe Chemistry project

#-----------------------------------------------------------------------------#
#   Title: Plot results of randomization inference
#  Author: B Saul
#    Date: 20191125
# Purpose: 
#-----------------------------------------------------------------------------#

library(ggplot2)
library(dplyr)
library(grid)
library(gridExtra)

source("programs/4_displays/display_functions.R")

vers    <- "V002"
outFile <- sprintf("manuscript/figures/ri_ncr_hypothesis_%s.pdf", vers)

dt <- 
  read_all_ri_data() %>%
  mutate(
    label    = purrr::map_chr(config, "label"),
    sublabel = purrr::map_chr(config, "sublabel"),
    desc     = purrr::map_chr(config, "desc"),
    contrast = purrr::map_chr(config, ~ purrr::chuck(.x, "filters", "contrast"))
  )

plot_dt <-
  dt %>%
  select(
    species, signal, element,
    label, contrast, test_data = sublabel, sublabel, hypothesis = desc,
    # nsims,
    # which_layer, which_annuli, which_agrp, which_annuli, test_data,
    # inner_buffer, outer_buffer, 
    p_value)  %>%
  filter(
    test_data %in% c("ri[ls]"),
    # label %in% c("D", "E", "B"),
    signal == "gam"
  ) %>%
  mutate(
    element2 = case_when(
      stringr::str_detect(element, "^(Zn|Cu|Mg)") ~ paste0(stringr::str_replace(element, "_ppm_m", "["), "]"),
      TRUE ~ stringr::str_remove(element, "_ppm_m.*")
    ),
    p_flag  = p_value < 0.1,
    p_small = (p_value < 0.001),
    p_value2 = if_else(p_small, 0.001, p_value)
  )



# ggplot(
#   data = plot_dt,
#   aes(x = label, y = element2, 
#       size = -log10(p_value+ 1),
#       color = -log10(p_value+ 1) )
# ) + 
#   geom_point() + 
#   scale_color_gradient(
#     low = "#e5f5f9", high = "#00441b"
#   ) +
#   facet_grid( ~ species)


## Plotting it ####

p1 <- single_ri_plot(filter(plot_dt, label == "A"))
p2 <- single_ri_plot(filter(plot_dt, label == "B"))
p3 <- single_ri_plot(filter(plot_dt, label == "C"))
# p4 <- single_ri_plot(filter(plot_dt, label == "D"))
p5 <- single_ri_plot(filter(plot_dt, label == "E"))

p <- 
grid.arrange(
  textGrob(
    "A",
    hjust = 0,
    x = 0),
  p1,
  textGrob(
    "B",
    hjust = 0,
    x = 0),
  p2,
  textGrob(
    "C",
    hjust = 0,
    x = 0),
  p3,
  textGrob(
    "D",
    hjust = 0,
    x = 0),
  p5,
  ncol = 1,
  heights = rep(c(0.2, 2), 4)
)



ggsave(
  file = outFile,
  p, width = 3, height = 6.6
)