diff options
Diffstat (limited to 'R/checksubstance.R')
| -rw-r--r-- | R/checksubstance.R | 158 |
1 files changed, 78 insertions, 80 deletions
diff --git a/R/checksubstance.R b/R/checksubstance.R index f22d4e2..e74ad21 100644 --- a/R/checksubstance.R +++ b/R/checksubstance.R @@ -1,97 +1,95 @@ -checksubstance <- function(substance, db = "cytotox", experimentator = "%", - celltype = "%", enzymetype = "%", organism = "%", - endpoint = "%", - whereClause = "1", ok= "%") +checksubstance <- function(substance, + db = c("cytotox", "enzymes", "ecotox"), + experimentator = "%", + celltype = "%", enzymetype = "%", organism = "%", + endpoint = "%", + whereClause = "1", ok= "%") { - databases <- data.frame( - responsename=c("viability","activity","response"), - testtype=c("celltype","enzyme","organism"), - exptype=c("plate","plate","experiment")) - rownames(databases) <- c("cytotox","enzymes","ecotox") + db = match.arg(db) - if (!(db %in% rownames(databases))) stop("Database is not supported") + databases <- data.frame( + responsename = c("viability", "activity", "raw_response"), + testtype = c("celltype", "enzyme", "organism"), + exptype = c("plate", "plate", "experiment"), + row.names = c("cytotox", "enzymes", "ecotox"), + stringsAsFactors = FALSE) - 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.") - } + con <- dbConnect(odbc(), "cytotox", database = db) - responsename = as.character(databases[db,1]) - testtype = as.character(databases[db,2]) - exptype = as.character(databases[db,3]) + responsename <- databases[db, 1] + testtype <- databases[db, 2] + exptype <- databases[db, 3] - if (db == "cytotox") { - type <- celltype - } - if (db == "enzymes") { - type <- enzymetype - } - if (db == "ecotox") { - type <- organism - } + 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", - " FROM ",db," WHERE substance LIKE '", - substance,"' AND experimentator LIKE '", - experimentator,"' AND ",testtype," LIKE '", - type,"' AND ", - whereClause," AND ok LIKE '",ok,"'", - sep = "") + query <- paste("SELECT experimentator,substance,", + testtype, ",", exptype, ",conc,unit,",responsename,",ok", + " FROM ",db," WHERE substance LIKE '", + substance,"' AND experimentator LIKE '", + experimentator,"' AND ",testtype," LIKE '", + type,"' AND ", + whereClause," AND ok LIKE '",ok,"'", + sep = "") - if (db == "ecotox") { - query <- paste(query, " AND type LIKE '", - endpoint, "'", sep = "") - } + if (db == "ecotox") { + query <- paste(query, " AND type LIKE '", + endpoint, "'", sep = "") + } - data <- RODBC::sqlQuery(channel,query) - RODBC::odbcClose(channel) + data <- dbGetQuery(con, query) - if (length(data$experimentator) < 1) { - stop(paste("\nNo response data for",substance,"in database", - db,"found with these parameters\n")) - } + if (length(data$experimentator) < 1) { + stop(paste("\nNo response data for",substance,"in database", + db,"found with these parameters\n")) + } - data$experimentator <- factor(data$experimentator) - data$substance <- factor(data$substance) - 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$ok <- factor(data$ok) + data$experimentator <- factor(data$experimentator) + data$substance <- factor(data$substance) + 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$ok <- factor(data$ok) - if (length(experiments)>6) { - palette(rainbow(length(experiments))) - } + if (length(experiments)>6) { + palette(rainbow(length(experiments))) + } - plot(log10(data$conc),data[[responsename]], - xlim=c(-2.5, 4.5), - ylim= range(data[[responsename]], na.rm = TRUE), - xlab=paste("decadic logarithm of the concentration in ",levels(data$unit)), - ylab=responsename) + plot(log10(data$conc),data[[responsename]], + xlim=c(-2.5, 4.5), + ylim= range(data[[responsename]], na.rm = TRUE), + xlab=paste("decadic logarithm of the concentration in ",levels(data$unit)), + ylab=responsename) - explist <- split(data,data[[exptype]]) + 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))) + 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)), - substring(exptype,2), sep = "") - experimentators <- paste(levels(data$experimentator), collapse = " ") - types <- paste(levels(data$type), collapse = " ") - experiments <- paste(levels(data[[exptype]]), collapse = " ") - class(experiments) - cat("\n\tSubstanz:\t\t",substance,"\n", - "\tExperimentator(s):\t", experimentators,"\n", - "\tType(s): \t\t",types,"\n", - "\tEndpoint: \t\t",endpoint,"\n", - "\t", exptypename, "(s):\t\t",experiments,"\n\n", sep = "") + exptypename <- paste(toupper(substring(exptype,1,1)), + substring(exptype,2), sep = "") + experimentators <- paste(levels(data$experimentator), collapse = " ") + types <- paste(levels(data$type), collapse = " ") + experiments <- paste(levels(data[[exptype]]), collapse = " ") + class(experiments) + cat("\n\tSubstanz:\t\t",substance,"\n", + "\tExperimentator(s):\t", experimentators,"\n", + "\tType(s): \t\t",types,"\n", + "\tEndpoint: \t\t",endpoint,"\n", + "\t", exptypename, "(s):\t\t",experiments,"\n\n", sep = "") } |