Report for positive controls for Vibrio fischeri

1 files changed, 50 insertions, 29 deletions

diff --git a/R/checkexperiment.R b/R/checkexperiment.R
index b69b81f..8c844e6 100644
--- a/R/checkexperiment.R
+++ b/R/checkexperiment.R
@@ -2,7 +2,7 @@ if(getRversion() >= '2.15.1') utils::globalVariables(c("type", "conc"))
 checkexperiment <- function(id, db = "ecotox", endpoint = "%")
 {
     databases <- data.frame(
-        responsename=c("viability","activity","response"),
+        responsename=c("viability","activity","raw_response"),
         testtype=c("celltype","enzyme","organism"),
         exptype=c("plate","plate","experiment"))
     rownames(databases) <- c("cytotox","enzymes","ecotox")
@@ -15,7 +15,6 @@ checkexperiment <- function(id, db = "ecotox", endpoint = "%")
       stop("For this function, the RODBC package has to be installed and configured.")
     }
 
-
     responsename = as.character(databases[db,1])
     testtype = as.character(databases[db,2])
     exptype = as.character(databases[db,3])
@@ -26,8 +25,8 @@ checkexperiment <- function(id, db = "ecotox", endpoint = "%")
     commentdata <- RODBC::sqlQuery(channel,commentquery)
     comment <- as.character(commentdata[[1]])
 
-    expquery <- paste("SELECT experimentator,substance, ",
-        testtype, ",conc,unit,", responsename, ",performed,ok",
+    expquery <- paste("SELECT experimentator, substance, ",
+        testtype, ", conc, unit,", responsename, ", performed, ok",
         " FROM ",db," WHERE ",exptype,"=", id,
             sep = "")
 
@@ -50,30 +49,55 @@ checkexperiment <- function(id, db = "ecotox", endpoint = "%")
     on.exit(par(op))
 
     if (db %in% c("cytotox","enzymes")) {
-        blinds <- subset(controldata,type=="blind")
-        controls <- subset(controldata,type=="control")
-
-        numberOfBlinds <- length(blinds$response)
-        meanOfBlinds <- signif(mean(blinds$response),2)
-        stdOfBlinds <- signif(sd(blinds$response),2)
+        blinds <- subset(controldata, type == "blind")
+        controls <- subset(controldata, type == "control")
+        QA <- matrix(nrow = 2, ncol = 4,
+            dimnames = list(c("Blind", "Control (conc = 0)"),
+                            c("Number", "Mean", "Std. Dev.", "% Std. Dev")))
+
+        QA[1, 1] <- length(blinds$response)
+        QA[1, 2] <- signif(mean(blinds$response), 2)
+        QA[1, 3] <- signif(sd(blinds$response), 2)
+        QA[1, 4] <-signif(QA[1, 3] * 100 / QA[1, 2],2)
     } else {
-        controls <- subset(expdata,conc == 0)
+        # Use raw response for ecotox
+        expdata$response <- expdata$raw_response
+
+        controls <- subset(expdata, conc == 0)
         expdata <- subset(expdata, conc != 0)
 
-        numberOfBlinds <- NA
-        meanOfBlinds <- NA
-        stdOfBlinds <- NA
+        QA <- matrix(nrow = 1, ncol = 4,
+            dimnames = list(c("Control (conc = 0)"),
+                            c("Number", "Mean", "Std. Dev.", "% Std. Dev")))
 
     }
+
     numberOfControls <- length(controls$response)
+    QA["Control (conc = 0)", 1] <- numberOfControls
     if (numberOfControls > 0) {
-        meanOfControls <- signif(mean(controls$response),2)
-        stdOfControls <- signif(sd(controls$response),2)
-        percentstdOfcontrols <-signif(stdOfControls *100/meanOfControls,2)
-    } else {
-        meanOfControls <- stdOfControls <- percentstdOfcontrols <- NA
+        QA["Control (conc = 0)", 2] <- signif(mean(controls$response),2)
+        QA["Control (conc = 0)", 3] <- signif(sd(controls$response),2)
+        QA["Control (conc = 0)", 4] <- signif(QA["Control (conc = 0)", 3] * 100 /
+                                              QA["Control (conc = 0)", 2],2)
     }
 
+    if (db == "ecotox") {
+        if (identical(as.character(levels(expdata$organism)), "Vibrio fischeri")) {
+            positive <- subset(expdata, substance == "Na Cl")
+            if (nrow(positive) > 0) {
+                 QA <- rbind(QA,
+                             c(nrow(positive),
+                               signif(mean(positive$raw_response), 2),
+                               signif(sd(positive$raw_response), 2),
+                               signif(100 * sd(positive$raw_response) /
+                                      mean(positive$raw_response), 2)))
+
+                 rownames(QA) <- c("Control (conc = 0)",
+                                   "Positive control (Na Cl)")
+            }
+            expdata <- subset(expdata, substance != "Na Cl", drop = TRUE)
+        }
+    }
 
     if (length(expdata$experimentator) < 1) {
         stop("There is no response data for ",exptype," ",
@@ -95,18 +119,15 @@ checkexperiment <- function(id, db = "ecotox", endpoint = "%")
         "\tSubstance(s):\t\t",levels(expdata$substance),"\n",
         "\tConcentration unit(s):\t",levels(expdata$unit),"\n",
         "\tComment:\t\t",comment,"\n",
-        "\tOK Levels:\t\t\t",levels(expdata$ok),"\n",
-        "\t\tNumber \tMean \tStd. Dev. \t% Std. Dev.\n",
-        "\tblind\t",numberOfBlinds,"\t",meanOfBlinds,"\t",stdOfBlinds,"\n",
-        "\tcontrol\t",numberOfControls,"\t",meanOfControls,"\t",
-            stdOfControls,"\t\t",percentstdOfcontrols,"\n")
+        "\tOK Levels:\t\t",levels(expdata$ok),"\n\n")
 
+    print(QA)
 
     if (db == "ecotox") {
         boxplot(controls$response,
             names="controls",
             ylab="Response",
-            ylim=c(0,max(controls$response)),
+            ylim=c(0, max(controls$response, na.rm = TRUE)),
             boxwex=0.4,
             main=paste("Plate ",id))
     } else {
@@ -125,10 +146,10 @@ checkexperiment <- function(id, db = "ecotox", endpoint = "%")
     lhd <- log10(max(drdata$conc))
 
     plot(1,type="n",
-        xlim=c(lld - 0.5, lhd + 2),
-        ylim= c(-0.1, 2),
-        xlab=paste("decadic logarithm of the concentration in ",levels(expdata$unit)),
-        ylab=responsename)
+        xlim = c(lld - 0.5, lhd + 2),
+        ylim = range(0, max(expdata[responsename])),
+        xlab = paste("decadic logarithm of the concentration in ",levels(expdata$unit)),
+        ylab = responsename)
 
     drdatalist <- split(drdata,drdata$substance)