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supplemental.R
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supplemental.R
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library(drake)
library(toxEval)
library(tidyverse)
loadd(chemicalSummary)
length(unique(chemicalSummary$endPoint))
end_point_info <- end_point_info
ep_we_use <- chemicalSummary %>%
select(endPoint) %>%
distinct() %>%
left_join(select(end_point_info,
endPoint = assay_component_endpoint_name,
assay = assay_source_long_name), by="endPoint")
any(ep_we_use$assay == "NHEERL Padilla Lab")
zebra <- chemicalSummary %>%
left_join(ep_we_use, by="endPoint") %>%
filter(assay == "NHEERL Padilla Lab")
######################################
# AOP Plot details
loadd(AOP)
threshold = 0.001
siteThreshold = 10
endpoints_sites_hits <- filter(chemicalSummary,EAR > 0) %>%
group_by(endPoint,site,date) %>%
summarize(EARsum = sum(EAR)) %>%
group_by(site,endPoint) %>%
summarize(EARmax = max(EARsum)) %>%
filter(EARmax >= threshold) %>%
group_by(endPoint) %>%
summarize(numSites = n_distinct(site)) %>%
arrange(desc(numSites)) %>%
filter(numSites >= siteThreshold)
priority_endpoints <- endpoints_sites_hits$endPoint
AOP_list <- AOP %>%
filter(endPoint %in% priority_endpoints) %>%
group_by(endPoint) %>%
summarize(n_AOPs = length(unique(ID)),
AOPs = list(unique(ID)))
nChems <- chemicalSummary %>%
filter(endPoint %in% priority_endpoints) %>%
group_by(endPoint) %>%
summarize(nChems = length(unique(chnm)),
Chemicals = list(unique(as.character(chnm))))
graphData <- chemicalSummary %>%
group_by(shortName,date,endPoint) %>%
summarise(sumEAR=sum(EAR)) %>%
group_by(shortName, endPoint) %>%
summarise(maxEAR=max(sumEAR))
orderColsBy <- graphData %>%
filter(endPoint %in% priority_endpoints) %>%
group_by(endPoint) %>%
summarise(median = quantile(maxEAR[maxEAR != 0],0.5)) %>%
arrange(median)
orderedLevelsEP <- orderColsBy$endPoint
aop_summary <- graphData %>%
ungroup() %>%
filter(maxEAR > 0) %>%
filter(endPoint %in% priority_endpoints) %>%
group_by(endPoint) %>%
summarise(medianEAR = median(maxEAR),
maxEAR = max(maxEAR),
n_sites = length(unique(shortName)),
sites = list(unique(shortName))) %>%
ungroup() %>%
left_join(AOP_list, by="endPoint") %>%
left_join(nChems, by="endPoint")
aop_summary$endPoint <- factor(aop_summary$endPoint, levels = orderedLevelsEP)
aop_summary <- arrange(aop_summary, desc(endPoint))
aop_summary$AOPs[sapply(aop_summary$AOPs, is.null)] <- NA
data.table::fwrite(aop_summary, "data/supplemental/aop_summary.txt", sep = "\t")