diff --git a/DESCRIPTION b/DESCRIPTION index 0eee63c7..319d67e6 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,7 +1,7 @@ Package: toxEval Type: Package Title: ToxCast Evaluations -Version: 0.3.8.9003 +Version: 0.3.8.9004 Date: 2017-10-04 Authors@R: c( person("Steven", "Corsi", role = c("aut"), email = "srcorsi@usgs.gov"), diff --git a/R/get_chemical_summary.R b/R/get_chemical_summary.R index 2b18d37e..04237288 100644 --- a/R/get_chemical_summary.R +++ b/R/get_chemical_summary.R @@ -73,30 +73,55 @@ get_chemical_summary <- function(ACClong, filtered_ep, graphData <- graph_chem_data(chemicalSummary) - orderClass <- graphData %>% + orderClass_df <- orderClass(graphData) + + orderChem_df <- orderChem(graphData, orderClass_df) + + chemicalSummary$chnm <- factor(chemicalSummary$chnm, + levels = orderChem_df$chnm) + + chemicalSummary$Class <- factor(chemicalSummary$Class, + levels = rev(levels(orderChem_df$Class))) + + return(chemicalSummary) +} + +#' orderClass +#' +#' @param graphData data frame +orderClass <- function(graphData){ + + chnm <- Class <- maxEAR <- median <- max_med <- ".dplyr" + + orderClass_df <- graphData %>% group_by(chnm, Class) %>% summarise(median = quantile(maxEAR[maxEAR != 0],0.5)) %>% group_by(Class) %>% summarise(max_med = max(median, na.rm = TRUE)) %>% arrange(desc(max_med)) - - orderChem <- graphData %>% + + return(orderClass_df) +} + +#' orderChem +#' +#' @param graphData data frame +#' @param orderClass_df data frame +orderChem <- function(graphData, orderClass_df){ + + chnm <- Class <- maxEAR <- median <- ".dplyr" + + orderChem_df <- graphData %>% group_by(chnm,Class) %>% summarise(median = quantile(maxEAR[maxEAR != 0],0.5)) %>% data.frame() %>% - mutate(Class = factor(Class, levels = rev(as.character(orderClass$Class)))) - - orderChem$median[is.na(orderChem$median)] <- 0 + mutate(Class = factor(Class, levels = rev(as.character(orderClass_df$Class)))) - orderChem <- arrange(orderChem, Class, median) - - chemicalSummary$chnm <- factor(chemicalSummary$chnm, - levels = orderChem$chnm) + orderChem_df$median[is.na(orderChem_df$median)] <- 0 - chemicalSummary$Class <- factor(chemicalSummary$Class, - levels = rev(levels(orderChem$Class))) + orderChem_df <- arrange(orderChem_df, Class, median) - return(chemicalSummary) + return(orderChem_df) } #' remove_flags diff --git a/man/orderChem.Rd b/man/orderChem.Rd new file mode 100644 index 00000000..bbece4e7 --- /dev/null +++ b/man/orderChem.Rd @@ -0,0 +1,16 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/get_chemical_summary.R +\name{orderChem} +\alias{orderChem} +\title{orderChem} +\usage{ +orderChem(graphData, orderClass_df) +} +\arguments{ +\item{graphData}{data frame} + +\item{orderClass_df}{data frame} +} +\description{ +orderChem +} diff --git a/man/orderClass.Rd b/man/orderClass.Rd new file mode 100644 index 00000000..7d35a0de --- /dev/null +++ b/man/orderClass.Rd @@ -0,0 +1,14 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/get_chemical_summary.R +\name{orderClass} +\alias{orderClass} +\title{orderClass} +\usage{ +orderClass(graphData) +} +\arguments{ +\item{graphData}{data frame} +} +\description{ +orderClass +}