Merge pull request #170 from ldecicco-USGS/master

ACC instead of AC50
DOI-USGS · Dec 21, 2016 · 173fabe · 173fabe
2 parents 5717980 + ff24fdc
commit 173fabe
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Showing 7 changed files with 68 additions and 9 deletions.
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,7 +1,7 @@
 Package: toxEval
 Type: Package
 Title: ToxCast Evaluations
-Version: 0.2.5
+Version: 0.2.6
 Date: 2016-10-19
 Authors@R: c( person("Steven", "Corsi", role = c("aut"),
     email = "[email protected]"),
@@ -22,7 +22,7 @@ Imports:
     tidyr,
     DT (>= 0.1.24),
     leaflet  (>= 1.0.0),
-    ggplot2,
+    ggplot2 (>= 2.2.0),
     gridExtra,
     grid,
     shiny,

diff --git a/NAMESPACE b/NAMESPACE
@@ -3,6 +3,7 @@
 export(AC10)
 export(AC50gain)
 export(AC50loss)
+export(ACC)
 export(chemSumm)
 export(chemSummBasic)
 export(endPointInfo)

diff --git a/R/sysdata.rda b/R/sysdata.rda
diff --git a/R/toxEval.R b/R/toxEval.R
@@ -54,10 +54,10 @@ NULL
 #'  \item{AC10}{AC10 endpoints}
 #'}
 #'
-#'@aliases AC50gain AC50loss AC10
+#'@aliases AC50gain AC50loss AC10 ACC
 #'@name Constants
 #'@docType data
-#'@export AC50gain AC50loss AC10
+#'@export AC50gain AC50loss AC10 ACC
 #'@keywords datasets
 #'@examples
 #'AC50GainColumns <- names(AC50gain)

diff --git a/inst/extdata/chemicalSummary_includesFlags.rds b/inst/extdata/chemicalSummary_includesFlags.rds
diff --git a/inst/shiny/server.R b/inst/shiny/server.R
@@ -17,6 +17,63 @@ endPointInfo <- endPointInfo[!(endPointInfo$assay_source_name == "NVS" & endPoin
 endPointInfo <- endPointInfo[endPointInfo$assay_component_endpoint_name != "TOX21_p53_BLA_p3_ratio",]
 endPointInfo <- endPointInfo[endPointInfo$assay_component_endpoint_name != "TOX21_p53_BLA_p2_viability",]
 
+endPointInfo$intended_target_family[endPointInfo$assay_component_endpoint_name %in% 
+                                      c("CLD_CYP1A1_24hr","CLD_CYP1A1_48hr","CLD_CYP1A1_6hr",
+                                        "CLD_CYP1A2_24hr","CLD_CYP1A2_48hr","CLD_CYP1A2_6hr")] <- "dna binding"
+
+endPointInfo$intended_target_family_sub[endPointInfo$assay_component_endpoint_name %in% 
+                                      c("CLD_CYP1A1_24hr","CLD_CYP1A1_48hr","CLD_CYP1A1_6hr",
+                                        "CLD_CYP1A2_24hr","CLD_CYP1A2_48hr","CLD_CYP1A2_6hr")] <- "basic helix-loop-helix protein"
+
+endPointInfo$intended_target_official_symbol[endPointInfo$assay_component_endpoint_name %in% 
+                                          c("CLD_CYP1A1_24hr","CLD_CYP1A1_48hr","CLD_CYP1A1_6hr",
+                                            "CLD_CYP1A2_24hr","CLD_CYP1A2_48hr","CLD_CYP1A2_6hr")] <- "AhR"
+
+endPointInfo$intended_target_family[endPointInfo$assay_component_endpoint_name %in% 
+                                      c("CLD_CYP2B6_24hr","CLD_CYP2B6_48hr","CLD_CYP2B6_6hr",
+                                        "CLD_CYP3A4_24hr","CLD_CYP3A4_48hr","CLD_CYP3A4_6hr",
+                                        "CLD_SULT2A_48hr","CLD_UGT1A1_48hr","NVS_NR_bER",
+                                        "NVS_NR_bPR","NVS_NR_cAR")] <- "nuclear receptor"
+
+endPointInfo$intended_target_family_sub[endPointInfo$assay_component_endpoint_name %in% 
+                                      c("CLD_CYP2B6_24hr","CLD_CYP2B6_48hr","CLD_CYP2B6_6hr",
+                                        "CLD_CYP3A4_24hr","CLD_CYP3A4_48hr","CLD_CYP3A4_6hr",
+                                        "CLD_SULT2A_48hr","CLD_UGT1A1_48hr")] <- "non-steroidal"
+
+endPointInfo$intended_target_official_symbol[endPointInfo$assay_component_endpoint_name %in% 
+                                    c("CLD_CYP2B6_24hr","CLD_CYP2B6_48hr","CLD_CYP2B6_6hr",
+                                      "CLD_SULT2A_48hr")] <- "NR1I3" 
+
+endPointInfo$intended_target_official_symbol[endPointInfo$assay_component_endpoint_name %in% 
+                                       c("CLD_CYP3A4_24hr","CLD_CYP3A4_48hr","CLD_CYP3A4_6hr",
+                                         "CLD_SULT2A_48hr")] <- "NR1I2" 
+
+endPointInfo$intended_target_family[endPointInfo$assay_component_endpoint_name %in% 
+                                      c("NVS_NR_bER", "NVS_NR_bPR","NVS_NR_cAR")] <- "steroidal"
+
+endPointInfo$intended_target_official_symbol[endPointInfo$assay_component_endpoint_name %in% 
+                                               c("NVS_NR_bER", "NVS_NR_bPR","NVS_NR_cAR")] <- c("ESR","PGR","AR")
+
+endPointInfo$intended_target_family[endPointInfo$assay_component_endpoint_name %in% 
+                                      c("Tanguay_ZF_120hpf_ActivityScore",
+                                        "Tanguay_ZF_120hpf_AXIS_up",
+                                        "Tanguay_ZF_120hpf_BRAI_up",
+                                        "Tanguay_ZF_120hpf_CFIN_up",
+                                        "Tanguay_ZF_120hpf_EYE_up",
+                                        "Tanguay_ZF_120hpf_JAW_up",
+                                        "Tanguay_ZF_120hpf_MORT_up",
+                                        "Tanguay_ZF_120hpf_OTIC_up",
+                                        "Tanguay_ZF_120hpf_PE_up",
+                                        "Tanguay_ZF_120hpf_PFIN_up",
+                                        "Tanguay_ZF_120hpf_PIG_up",
+                                        "Tanguay_ZF_120hpf_SNOU_up",
+                                        "Tanguay_ZF_120hpf_SOMI_up",
+                                        "Tanguay_ZF_120hpf_SWIM_up",
+                                        "Tanguay_ZF_120hpf_TR_up",
+                                        "Tanguay_ZF_120hpf_TRUN_up",
+                                        "Tanguay_ZF_120hpf_YSE_up")] <- "zebrafish"
+
+
 choicesPerGroup <- apply(endPointInfo, 2, function(x) length(unique(x[!is.na(x)])))
 choicesPerGroup <- which(choicesPerGroup > 6 & choicesPerGroup < 100)
 
@@ -242,7 +299,7 @@ shinyServer(function(input, output,session) {
     # )
 
     if (input$data == "Water Sample"){
-      chemicalSummary <- readRDS(file.path(pathToApp,"chemicalSummary_includesFlags.rds"))
+      chemicalSummary <- readRDS(file.path(pathToApp,"chemicalSummary_ACC.rds"))
       stationINFO <<- readRDS(file.path(pathToApp,"sitesOWC.rds"))
     } else if (input$data == "Passive Samples"){
       chemicalSummary <- readRDS(file.path(pathToApp,"chemicalSummaryPassive.rds"))
@@ -736,11 +793,11 @@ shinyServer(function(input, output,session) {
               legend.background = element_rect(colour = 'black', fill = 'white')) 
     }
 
-    ymin <<- 10^(ggplot_build(lowerPlot)$panel$ranges[[1]]$y.range)[1]
-    ymax <<- 10^(ggplot_build(lowerPlot)$panel$ranges[[1]]$y.range)[2]
+    ymin <<- 10^(ggplot_build(lowerPlot)$layout$panel_ranges[[1]]$y.range)[1]
+    ymax <<- 10^(ggplot_build(lowerPlot)$layout$panel_ranges[[1]]$y.range)[2]
 
-    xmax <<- ggplot_build(lowerPlot)$panel$ranges[[1]]$x.range[2]
-    xmin <<- ggplot_build(lowerPlot)$panel$ranges[[1]]$x.range[1]
+    xmax <<- ggplot_build(lowerPlot)$layout$panel_ranges[[1]]$x.range[2]
+    xmin <<- ggplot_build(lowerPlot)$layout$panel_ranges[[1]]$x.range[1]
 
     lowerPlot <- lowerPlot + 
       geom_text(data=data.frame(), aes(x=namesToPlot, y=ymin,label=nSamples),size=5)  +

diff --git a/man/Constants.Rd b/man/Constants.Rd