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plot_stack_figure.R
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plot_stack_figure.R
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library(drake)
library(tidyverse)
library(toxEval)
library(ggpubr)
source(file = "R/report/stack_plots.R")
source(file = "R/report/combo_plot2.R")
source(file = "R/analyze/table_chem_class_Land_use_correlation.R")
source(file = "read_chemicalSummary.R")
loadd(site_info)
loadd(tox_list)
lakes_ordered <- c("Lake Superior",
"Lake Michigan",
"Lake Huron",
"Lake Erie",
"Lake Ontario")
df <- Chem_Class_correlation_table()
df <- tibble(x = 0.95,
y = 0.95,
site_grouping = factor("Lake Superior",
levels = lakes_ordered),
tb = list(df))
color_map <- class_colors(tox_list)
font_size <- 5
upperPlot <- plot_tox_stacks_manuscript2(chemical_summary = chemicalSummary,
chem_site = site_info,
title=NA,cbValues = color_map,
font_size = font_size,
category = "Chemical Class")
library(ggpmisc)
stack2 <- upperPlot +
geom_table_npc(data = df,
aes(npcx = x,
npcy = y,
label = tb), size = 1.5,
hjust = 1, vjust = 1)
ggsave(stack2, filename = "plots/new_stack_w_table.pdf", height = 8, width = 5)
ggsave(stack2, filename = file.path(Sys.getenv("PASSIVE_PATH"),
"Figures/Polished figures/new_stack_w_table.pdf"),
height = 8, width = 5)
full_plot <- whole_stack(chemicalSummary, site_info, title=NA,
tox_list, color_map, font_size,
category = "Chemical Class")
pdf("plots/stack_full.pdf", width = 5.5, height =7, onefile=FALSE)
ggarrange(
full_plot$chem_count,
full_plot$no_axis +
ylab("Sum of Maximum EAR Values"),
widths = c(1.2,5),
common.legend = TRUE, legend = "bottom"
)
dev.off()
levels(chemicalSummary$Class)[levels(chemicalSummary$Class) == "Food Additive/Plasticizer"] <- "Food Additive"
levels(chemicalSummary$Class)[levels(chemicalSummary$Class) == "Antimicrobial disinfectant"] <- "Antimicrobial"
tox_list$chem_info$Class[tox_list$chem_info$Class == "Food Additive/Plasticizer"] <- "Food Additive"
tox_list$chem_info$Class[tox_list$chem_info$Class == "Antimicrobial disinfectant"] <- "Antimicrobial"
classes <- unique(tox_list$chem_info$Class)
num_chem_to_keep <- 5
font_size <- 5
pdf("plots/classes_split_new.pdf", width = 6, height = 7, onefile=TRUE)
for(i in classes){
chem_i <- dplyr::filter(chemicalSummary, Class == i)
if(nrow(chem_i) == 0){
next
}
chem_i$chnm <- droplevels(chem_i$chnm)
if(length(levels(chem_i$chnm)) > num_chem_to_keep){
too_small <- levels(chem_i$chnm)[1:(length(levels(chem_i$chnm))-num_chem_to_keep)]
just_right <- levels(chem_i$chnm)[(length(levels(chem_i$chnm))-num_chem_to_keep+1):length(levels(chem_i$chnm))]
too_small_text <- paste0("Other [",length(too_small),"]")
chem_i$chnm <- as.character(chem_i$chnm)
chem_i$chnm[chem_i$chnm %in% too_small] <- too_small_text
chem_i$chnm <- factor(chem_i$chnm, levels = c(rev(just_right), too_small_text))
} else {
chem_i$chnm <- factor(as.character(chem_i$chnm), levels = rev(levels(chem_i$chnm)))
}
color_i <- colorspace::rainbow_hcl(length(unique(chem_i$chnm)),
start = -360, end = -55, c = 100, l = 64)
names(color_i) <- levels(chem_i$chnm)
if(grepl("Other",names(color_i)[length(color_i)])){
color_i[length(color_i)] <- "grey77"
}
class_plot <- whole_stack(chem_i, site_info, tox_list,
color_i, font_size,
category = "Chemical",
title = i)
i <- gsub("/","_",i)
# pdf(paste0(i,".pdf"), width = 4.5, height = 5.5, onefile=FALSE)
print(
ggarrange(
class_plot$chem_count,
class_plot$no_axis +
ylab("Sum of Maximum EAR Values"),
widths = c(1.3,5),
common.legend = TRUE, legend = "bottom"
))
}
dev.off()
class_plots <- list()
site_info <- site_info %>% arrange(`Short Name`)
levels(site_info$`Short Name`) <- paste0(levels(site_info$`Short Name`),
" (",site_info$map_nm,")")
font_size <- 8
for(i in classes){
chem_i <- chemicalSummary %>%
dplyr::filter(Class == i)
if(nrow(chem_i) == 0){
next
}
chem_i$chnm <- droplevels(chem_i$chnm)
if(length(levels(chem_i$chnm)) > num_chem_to_keep){
too_small <- levels(chem_i$chnm)[1:(length(levels(chem_i$chnm))-num_chem_to_keep)]
just_right <- levels(chem_i$chnm)[(length(levels(chem_i$chnm))-num_chem_to_keep+1):length(levels(chem_i$chnm))]
too_small_text <- paste0("Other [",length(too_small),"]")
chem_i$chnm <- as.character(chem_i$chnm)
chem_i$chnm[chem_i$chnm %in% too_small] <- too_small_text
chem_i$chnm <- factor(chem_i$chnm, levels = c(rev(just_right), too_small_text))
} else {
chem_i$chnm <- factor(as.character(chem_i$chnm), levels = rev(levels(chem_i$chnm)))
}
color_i <- colorspace::rainbow_hcl(length(unique(chem_i$chnm)),
start = -360, end = -55,
c = 100, l = 64)
names(color_i) <- levels(chem_i$chnm)
if(grepl("Other",names(color_i)[length(color_i)])){
color_i[length(color_i)] <- "grey77"
}
class_plots[[i]] <- whole_stack(chem_i, site_info, tox_list,
color_i, font_size,
category = "Chemical",
title = i)
}
library(cowplot)
general_lp <- c(0.1,0.87)
pdf("plots/MoreChemicalStacks_new.pdf", width = 10, height = 8)
rel_widths <- c(3.75,3,rep(c(1,3),3), 1, 3.5)
plot_grid(
class_plots[[1]]$chem_count,
class_plots[[1]]$no_axis +
theme(legend.position = general_lp,
strip.text.y = element_blank()) +
ylab(""),
class_plots[[2]]$chem_count +
theme(axis.text.y = element_blank()),
class_plots[[2]]$no_axis +
theme(legend.position = c(0.1,0.92) ,
strip.text.y = element_blank()) +
ylab(""),
class_plots[[3]]$chem_count +
theme(axis.text.y = element_blank()),
class_plots[[3]]$no_axis +
theme(legend.position = general_lp,
strip.text.y = element_blank()) +
ylab("Sum of Maximum EAR Values"),
class_plots[[4]]$chem_count +
theme(axis.text.y = element_blank()),
class_plots[[4]]$no_axis +
theme(legend.position = general_lp,
strip.text.y = element_blank()) +
ylab(""),
class_plots[[5]]$chem_count +
theme(axis.text.y = element_blank()),
class_plots[[5]]$no_axis +
theme(legend.position = c(0.01,0.84),
strip.text.y = element_text(size = 0.75*font_size)) +
ylab(""),
rel_widths = rel_widths,
nrow = 1
)
plot_grid(
class_plots[[6]]$chem_count,
class_plots[[6]]$no_axis +
theme(legend.position = c(0.05,0.87),
strip.text.y = element_blank()) +
ylab(""),
class_plots[[7]]$chem_count +
theme(axis.text.y = element_blank()),
class_plots[[7]]$no_axis +
theme(legend.position = general_lp ,
strip.text.y = element_blank()) +
ylab(""),
class_plots[[8]]$chem_count +
theme(axis.text.y = element_blank()),
class_plots[[8]]$no_axis +
theme(legend.position = general_lp,
strip.text.y = element_blank()) +
ylab("Sum of Maximum EAR Values"),
class_plots[[9]]$chem_count +
theme(axis.text.y = element_blank()),
class_plots[[9]]$no_axis +
theme(legend.position = general_lp,
strip.text.y = element_blank()) +
ylab(""),
class_plots[[10]]$chem_count +
theme(axis.text.y = element_blank()),
class_plots[[10]]$no_axis +
theme(legend.position = c(0.01,0.84),
strip.text.y = element_text(size = 0.75*font_size)) +
ylab(""),
rel_widths = rel_widths,
nrow = 1
)
plot_grid(
class_plots[[11]]$chem_count,
class_plots[[11]]$no_axis +
theme(legend.position = general_lp,
strip.text.y = element_blank()) +
ylab(""),
class_plots[[12]]$chem_count +
theme(axis.text.y = element_blank()),
class_plots[[12]]$no_axis +
theme(legend.position = general_lp ,
strip.text.y = element_blank()) +
ylab(""),
class_plots[[13]]$chem_count +
theme(axis.text.y = element_blank()),
class_plots[[13]]$no_axis +
theme(legend.position = general_lp,
strip.text.y = element_blank()) +
ylab("Sum of Maximum EAR Values"),
class_plots[[14]]$chem_count +
theme(axis.text.y = element_blank()),
class_plots[[14]]$no_axis +
theme(legend.position = c(0.01,0.92),
strip.text.y = element_blank()) +
ylab(""),
class_plots[[15]]$chem_count +
theme(axis.text.y = element_blank()),
class_plots[[15]]$no_axis +
theme(legend.position = c(0.01,0.88),
strip.text.y = element_text(size = 0.75*font_size)) +
ylab(""),
rel_widths = rel_widths,
nrow = 1
)
dev.off()
# Mock up stack of concentrations that aren't in toxCast:
loadd(chemicalSummary)
loadd(chemicalSummary_conc)
loadd(site_info)
loadd(tox_list)
non_tox <- chemicalSummary_conc %>%
filter(!(CAS %in% chemicalSummary$CAS))
source(file = "R/report/stack_plots.R")
source(file = "R/report/combo_plot2.R")
color_map <- class_colors(tox_list)
font_size <- 5
full_plot <- whole_stack(non_tox, site_info, title="Chemicals not in toxCast",
tox_list, color_map, font_size,
category = "Chemical Class")
pdf("plots/conc_stack_nonTox.pdf", width = 5.5, height =7, onefile=FALSE)
ggarrange(
full_plot$chem_count,
full_plot$no_axis +
ylab("Concentration [\U003BCg/L]"),
widths = c(1.2,5),
common.legend = TRUE, legend = "bottom"
)
dev.off()