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create_triple_fig.R
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create_triple_fig.R
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library(tidyverse)
library(toxEval)
library(cowplot)
library(ggplot2)
library(ggpubr)
library(readxl)
path_to_data <- Sys.getenv("PASSIVE_PATH")
create_triple_fig <- function(path_to_data){
tox_list <- create_toxEval(file.path(path_to_data,
"data","data_for_git_repo","clean",
"passive.xlsx"))
source(file = "R/analyze/get_sites_ready.R")
site_info <- prep_site_list(tox_list$chem_site)
cas_final <- readRDS(file.path(path_to_data,
"data","data_for_git_repo","clean",
"cas_df.rds"))
tox_list_concentrations <- readRDS(file.path(path_to_data,
"data","data_for_git_repo","clean",
"tox_list_concentrations.rds"))
graphData_tox_det <- readRDS(file.path(path_to_data,
"data", "data_for_git_repo",
"clean","graphData_tox_det.rds"))
graphData_conc_det_match <- readRDS(file.path(path_to_data,
"data", "data_for_git_repo",
"clean","graphData_conc_det_match.rds"))
axis_num <- 6
source(file = "R/report/combo_plot2.R")
#########################################
# # Get PCB?
# source(file = "R/analyze/data_reader.R")
# cas_df <- all_cas("data/raw/cas.xlsx")
# x <- generic_file_opener(file_name = file.path(Sys.getenv("PASSIVE_PATH"),
# "data","data_for_git_repo","raw",
# "general_2014.xlsx"),
# cas_df,
# n_max = 45,
# sheet = "OC-PCB-PBDE",
# site_sheet = "site info",
# year = 2014) %>%
# filter(chnm %in% "Total Pcbs")
#
# pcb <- data.frame(CAS = "1336-36-3",
# chnm = "Total PCBs",
# Class = "PCBs",
# stringsAsFactors = FALSE)
#
# tox_list_concentrations$chem_info <- bind_rows(tox_list_concentrations$chem_info,
# pcb)
#
# data_pcb <- x %>%
# select(SiteID, `Sample Date`, CAS, Value, comment )
#
# tox_list_concentrations$chem_data <- bind_rows(tox_list_concentrations$chem_data,
# data_pcb)
# tox_list_concentrations$benchmarks <- bind_rows(tox_list_concentrations$benchmarks,
# mutate(pcb,
# endPoint = "Concentration",
# ACC_value = 1,
# groupCol = "Concentration"))
# cas_final <- bind_rows(cas_final,
# pcb)
chemicalSummary_conc <- get_chemical_summary(tox_list_concentrations)
#######################
chemicalSummary_conc_no_match = chemicalSummary_conc %>%
filter(!(CAS %in% unique(graphData_tox_det$CAS)),
EAR > 0)
graphData_conc_no_match = graph_chem_data_CAS(chemicalSummary_conc_no_match) %>%
mutate(guide_side = "Concentration [\U003BCg/L]") %>%
left_join(select(cas_final, CAS, chnm), by="CAS")
full_classes <- c(levels(graphData_tox_det$Class),
levels(graphData_conc_no_match$Class)[!(levels(graphData_conc_no_match$Class) %in% levels(graphData_tox_det$Class))])
graphData_tox_det$Class <- factor(as.character(graphData_tox_det$Class), levels = full_classes)
graphData_conc_no_match$Class <- factor(as.character(graphData_conc_no_match$Class), levels = full_classes)
matches <- fancy_combo(graphData_tox_det,
graphData_conc_det_match,
tox_list,
axis_size = axis_num)
n_chems_matches <- length(unique(graphData_tox_det$chnm))
graphData_empty <- graphData_conc_no_match[FALSE,]
gd_no_match <- combine_gd(graphData_conc_no_match, graphData_empty)
n_chems_no_match <- length(unique(gd_no_match$chnm))
color_map <- class_colors(chemicalSummary_conc)
toxPlot_no_match <- combo_plot_matches_2(gd_no_match,
axis_size = axis_num,
color_map)
text_df_c <- label_info(gd_no_match, labels_to_use = "C")
toxPlot_no_match_w_lab <- add_label(toxPlot_no_match, text_df_c)
no_axis_no_match <- strip_graph(toxPlot_no_match_w_lab)
site_counts_df_no_match <- site_counts(tox_list_concentrations$chem_data, no_axis_no_match$data)
site_graph_no_match <- site_count_plot(site_counts_df_no_match,
axis_size = axis_num)
l2 <- get_legend(toxPlot_no_match)
plot_out <- plot_grid(
matches$site_graph,
matches$no_axis,
plot_grid(
plot_grid(
site_graph_no_match,
no_axis_no_match,
ncol = 2,
rel_widths = c(2.25,3)
),
plot_grid(
l2,
NULL,
ncol=1
),
nrow = 2, ncol = 1,
rel_heights = c(n_chems_no_match,n_chems_matches-n_chems_no_match)
),
rel_widths = c(2.75,4,5),
nrow=1,ncol=3
)
return(plot_out)
}
# pdf(file.path(Sys.getenv("PASSIVE_PATH"),"Figures/Polished figures/triple_graph.pdf"),
# width = 9, height = 11, onefile=FALSE)
# create_triple_fig()
# dev.off()