diff options
Diffstat (limited to 'R/checksubstance.R')
| -rw-r--r-- | R/checksubstance.R | 54 |
1 files changed, 27 insertions, 27 deletions
diff --git a/R/checksubstance.R b/R/checksubstance.R index 790182f..06cc635 100644 --- a/R/checksubstance.R +++ b/R/checksubstance.R @@ -1,7 +1,7 @@ checksubstance <- function(substance, db = "cytotox", experimentator = "%", - celltype = "%", enzymetype = "%", organism = "%", + celltype = "%", enzymetype = "%", organism = "%", endpoint = "%", - whereClause = "1", ok= "%") + whereClause = "1", ok= "%") { databases <- data.frame( responsename=c("viability","activity","response"), @@ -11,7 +11,7 @@ checksubstance <- function(substance, db = "cytotox", experimentator = "%", if (!(db %in% rownames(databases))) stop("Database is not supported") - if (require("RODBC")) { + if (requireNamespace("RODBC")) { channel <- RODBC::odbcConnect(db, uid="cytotox", pwd="cytotox", case="tolower") } else { stop("For this function, the RODBC package has to be installed and configured.") @@ -23,13 +23,13 @@ checksubstance <- function(substance, db = "cytotox", experimentator = "%", if (db == "cytotox") { type <- celltype - } + } if (db == "enzymes") { type <- enzymetype - } + } if (db == "ecotox") { type <- organism - } + } query <- paste("SELECT experimentator,substance,", testtype, ",", exptype, ",conc,unit,",responsename,",ok", @@ -41,7 +41,7 @@ checksubstance <- function(substance, db = "cytotox", experimentator = "%", sep = "") if (db == "ecotox") { - query <- paste(query, " AND type LIKE '", + query <- paste(query, " AND type LIKE '", endpoint, "'", sep = "") } @@ -51,39 +51,39 @@ checksubstance <- function(substance, db = "cytotox", experimentator = "%", if (length(data$experimentator) < 1) { stop(paste("\nNo response data for",substance,"in database", db,"found with these parameters\n")) - } - - data$experimentator <- factor(data$experimentator) + } + + data$experimentator <- factor(data$experimentator) data$substance <- factor(data$substance) - substances <- levels(data$substance) - data$type <- factor(data[[testtype]]) - data[[exptype]] <- factor(data[[exptype]]) + substances <- levels(data$substance) + data$type <- factor(data[[testtype]]) + data[[exptype]] <- factor(data[[exptype]]) experiments <- levels(data[[exptype]]) concentrations <- split(data$conc,data$conc) concentrations <- as.numeric(names(concentrations)) - data$unit <- factor(data$unit) + data$unit <- factor(data$unit) data$ok <- factor(data$ok) if (length(experiments)>6) { - palette(rainbow(length(experiments))) + palette(rainbow(length(experiments))) } - + plot(log10(data$conc),data[[responsename]], - xlim=c(-2.5, 4.5), - ylim= c(-0.1, 2), - xlab=paste("decadic logarithm of the concentration in ",levels(data$unit)), - ylab=responsename) - + xlim=c(-2.5, 4.5), + ylim= c(-0.1, 2), + xlab=paste("decadic logarithm of the concentration in ",levels(data$unit)), + ylab=responsename) + explist <- split(data,data[[exptype]]) - - for (i in 1:length(explist)) { - points(log10(explist[[i]]$conc),explist[[i]][[responsename]],col=i); - } - + + for (i in 1:length(explist)) { + points(log10(explist[[i]]$conc),explist[[i]][[responsename]],col=i); + } + legend("topleft", experiments, pch=1, col=1:length(experiments), inset=0.05) title(main=paste(substance," - ",levels(data$experimentator)," - ",levels(data$type))) - exptypename <- paste(toupper(substring(exptype,1,1)), + exptypename <- paste(toupper(substring(exptype,1,1)), substring(exptype,2), sep = "") experimentators <- paste(levels(data$experimentator), collapse = " ") types <- paste(levels(data$type), collapse = " ") |