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Merge branch 'dev' into 215-add-ggplot-output-option-to-tcplPlot
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cthunes authored Sep 6, 2024
2 parents 9bd0208 + 80c08b2 commit f87907c
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2 changes: 1 addition & 1 deletion .Rbuildignore
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Expand Up @@ -6,7 +6,7 @@
^inst/sql/create_sql_files\.R$
man-roxygen
tcpl.Rcheck
README.md
^README\.Rmd$
CONTRIBUTING.md
cran-comments.md
^CRAN-RELEASE$
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2 changes: 1 addition & 1 deletion .github/workflows/test-on-PR.yaml
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Expand Up @@ -2,7 +2,7 @@
# Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
on:
pull_request:
branches: [main]
branches: [main, dev]

name: test-coverage

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29 changes: 14 additions & 15 deletions DESCRIPTION
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Expand Up @@ -2,30 +2,28 @@ Package: tcpl
Title: ToxCast Data Analysis Pipeline
Version: 3.1.0
Authors@R: c(
person("Richard S", "Judson",role = c("ctb","ths"), email = "[email protected]"),
person("Dayne L", "Filer", role = "aut",email = "[email protected]"),
person("Jason","Brown",role = "cre", email = "[email protected]"),
person("Sarah E","Davidson-Fritz",role = "ctb",email = "[email protected]", comment = c(ORCID = "0000-0002-2891-9380")),
person("Richard S", "Judson",role = c("ctb","ths"), comment = c(ORCID = "0000-0002-2348-9633")),
person("Dayne L", "Filer", role = "aut"),
person("Jason","Brown", role = "cre", email = "[email protected]", comment = c(ORCID = "0009-0000-2294-641X")),
person("Sarah E","Davidson-Fritz", role = "ctb",email = "[email protected]", comment = c(ORCID = "0000-0002-2891-9380")),
person("Madison","Feshuk",role = "ctb",email = "[email protected]", comment = c(ORCID = "0000-0002-1390-6405")),
person("Lori","Kolaczkowski",role = "ctb",email = "[email protected]"),
person("Kurt", "Dunham", role = "ctb", email = "[email protected]"),
person("Carter", "Thunes", role = "ctb", email = "[email protected]"),
person("Ashley", "Ko", role = "ctb", email = "[email protected]"),
person("Todd", "Zurlinden", role="ctb"),
person("Kelly", "Carstens", role = "ctb", email = "[email protected]", comment = c(ORCID = "0000-0002-1746-5379")),
person("Todd", "Zurlinden", role="ctb", comment = c(ORCID = "0000-0003-1372-3913")),
person("Lori","Kolaczkowski",role = "ctb"),
person("Kurt", "Dunham", role = "ctb"),
person("Parth", "Kothiya", role = "ctb"),
person("Woodrow R", "Setzer", role = "ctb"),
person("Matthew T", "Martin", role = c("ctb", "ths")),
person("Katie", "Paul Friedman", role=c("ctb"), email = "[email protected]", comment = c(ORCID = "0000-0002-2710-1691"))
)
Description: A set of tools for processing and modeling high-throughput and
high-content chemical screening data. The package was developed for the
the chemical screening data generated by the US EPA ToxCast program, but
can be used for diverse chemical screening efforts.
URL: https://github.com/USEPA/CompTox-ToxCast-tcpl
Description: The ToxCast Data Analysis Pipeline (tcpl) is an R package that manages, curve-fits, plots, and stores ToxCast data to populate its linked MySQL database, invitrodb. The package was developed for the chemical screening data curated by the US EPA's Toxicity Forecaster (ToxCast) program, but tcpl can be used to support diverse chemical screening efforts.
URL: https://github.com/USEPA/CompTox-ToxCast-tcpl, https://www.epa.gov/comptox-tools/toxicity-forecasting-toxcast
Depends:
R (>= 3.5.0)
Imports:
data.table (>= 1.9.4),
data.table (>= 1.15.0),
DBI,
RMariaDB,
numDeriv,
Expand All @@ -44,7 +42,7 @@ Imports:
gridExtra,
stringr,
rlang,
ccdR
ctxR
Suggests:
roxygen2,
knitr,
Expand All @@ -58,7 +56,8 @@ Suggests:
colorspace,
magrittr,
vdiffr,
httptest
httptest,
rmdformats
License: MIT + file LICENSE
LazyData: true
RoxygenNote: 7.3.1
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10 changes: 5 additions & 5 deletions NAMESPACE
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Expand Up @@ -8,7 +8,6 @@ export(tcplAddModel)
export(tcplCode2CASN)
export(tcplConf)
export(tcplConfDefault)
export(tcplConfExample)
export(tcplConfList)
export(tcplConfLoad)
export(tcplConfReset)
Expand All @@ -26,7 +25,7 @@ export(tcplLoadAeid)
export(tcplLoadAid)
export(tcplLoadAsid)
export(tcplLoadChem)
export(tcplLoadClib)
export(tcplLoadChemList)
export(tcplLoadData)
export(tcplLvlCount)
export(tcplMakeAeidMultiPlts)
Expand All @@ -43,6 +42,7 @@ export(tcplObjHill)
export(tcplPlot)
export(tcplPlotFitc)
export(tcplPlotFits)
export(tcplPlotLoadData)
export(tcplPlotM4ID)
export(tcplPlotPlate)
export(tcplPrepOtpt)
Expand All @@ -62,9 +62,9 @@ import(gridExtra)
import(stringr)
importFrom(RColorBrewer,brewer.pal)
importFrom(RMariaDB,MariaDB)
importFrom(ccdR,get_all_assays)
importFrom(ccdR,get_bioactivity_details_batch)
importFrom(ccdR,register_ccdr)
importFrom(ctxR,get_all_assays)
importFrom(ctxR,get_bioactivity_details_batch)
importFrom(ctxR,register_ctx_api_key)
importFrom(dplyr,"%>%")
importFrom(dplyr,.data)
importFrom(dplyr,all_of)
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11 changes: 2 additions & 9 deletions R/assay_funcs.R
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Expand Up @@ -19,12 +19,7 @@
#' return the assay source ID (asid) and assay source name (asnm).
#'
#' @examples
#' ## Store the current config settings, so they can be reloaded at the end
#' ## of the examples
#' conf_store <- tcplConfList()
#' TCPLlite <- file.path(system.file(package = "tcpl"), "example")
#' tcplConf(db = TCPLlite, user = NA, host = NA, drvr = "tcplLite")
#'
#' \dontrun{
#' ## The load assay functions can be used without any parameters to list the
#' ## full list of registered assay elements:
#' tcplLoadAsid()
Expand All @@ -43,9 +38,7 @@
#' a1 <- tcplLoadAeid(fld = "anm", val = "Steroidogenesis")
#' a2 <- tcplLoadAeid(fld = "assay_name", val = "Steroidogenesis")
#' identical(a1, a2)
#'
#' ## Reset configuration
#' options(conf_store)
#' }
#'
#' @return A data.table containing the ID, name, and any additional fields.
NULL
11 changes: 6 additions & 5 deletions R/chemQueries.R
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Expand Up @@ -61,18 +61,19 @@
#-------------------------------------------------------------------------------

#-------------------------------------------------------------------------------
# .ClibQ: Create tcplLoadClib query string
# .ChemListQ: Create tcplLoadChemList query string
#-------------------------------------------------------------------------------

.ClibQ <- function(field, val) {
.ChemListQ <- function(field, val) {

qformat <- "SELECT chid, clib FROM chemical_library"
qformat <- "SELECT * FROM chemical_lists"

if (!is.null(field)) {

nfld <- switch(field,
chid = "chid",
clib = "clib")
dsstox_substance_id = "dsstox_substance_id",
list_acronym = "list_acronym")

qformat <- paste(qformat, "WHERE %s IN (%s);")
qstring <- sprintf(qformat, nfld, paste0("\"", val, "\"", collapse = ","))
Expand All @@ -88,6 +89,6 @@
}

#-------------------------------------------------------------------------------
# END .ClibQ
# END .ChemListQ
#-------------------------------------------------------------------------------

7 changes: 3 additions & 4 deletions R/config_funcs.R
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Expand Up @@ -14,8 +14,8 @@
#' @param ... Additional arguments that should be passed to dbConnect function
#'
#' @details
#' Currently, the tcpl package only supports the "MySQL" and "tcplLite" database
#' drivers.
#' Currently, the tcpl package supports the "MySQL", "example", and "API"
#' database drivers.
#'
#' The settings can be stored in a configuration file to make the using the
#' package more user-friendly. To create the configuration file, the user must
Expand Down Expand Up @@ -48,8 +48,7 @@
#' configuration file.
#'
#' \code{tcplConfDefault} changes the \code{options} to reflect the default
#' settings for the example tcplLite database, i.e. local directory, but does
#' not alter the configuration file.
#' settings for the API connection, but does not alter the configuration file.
#'
#' \code{tcplConfReset} is used to generate the initial configuration script,
#' and can be used to reset or regenerate the configuration script by the user.
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