diff options
| -rw-r--r-- | R/checkexperiment.R | 79 |
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) |