1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
|
if(getRversion() >= '2.15.1') utils::globalVariables(c("type", "conc", "substance"))
checkexperiment <- function(id, db = "ecotox", endpoint = "%")
{
databases <- data.frame(
responsename=c("viability","activity","raw_response"),
testtype=c("celltype","enzyme","organism"),
exptype=c("plate","plate","experiment"))
rownames(databases) <- c("cytotox","enzymes","ecotox")
if (!(db %in% rownames(databases))) stop("Database is not supported")
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.")
}
responsename = as.character(databases[db,1])
testtype = as.character(databases[db,2])
exptype = as.character(databases[db,3])
exptable <- paste(exptype, "s", sep="")
commentquery <- paste("SELECT comment FROM ", exptable ,
" WHERE ", exptype, " = ", id)
commentdata <- RODBC::sqlQuery(channel,commentquery)
comment <- as.character(commentdata[[1]])
expquery <- paste("SELECT experimentator, substance, ",
testtype, ", conc, unit,", responsename, ", performed, ok",
" FROM ",db," WHERE ",exptype,"=", id,
sep = "")
if (db == "ecotox") {
expquery <- paste(expquery, " AND type LIKE '",
endpoint, "'", sep = "")
}
expdata <- RODBC::sqlQuery(channel,expquery)
if (db %in% c("cytotox","enzymes")) {
controlquery <- paste("SELECT type,response FROM controls
WHERE plate=",id)
controldata <- RODBC::sqlQuery(channel,controlquery)
}
RODBC::odbcClose(channel)
op <- par(ask=TRUE)
on.exit(par(op))
if (db %in% c("cytotox","enzymes")) {
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$response), 2)
QA[1, 4] <-signif(QA[1, 3] * 100 / QA[1, 2],2)
} else {
# Use raw response for ecotox
expdata$response <- expdata$raw_response
controls <- subset(expdata, conc == 0)
expdata <- subset(expdata, conc != 0)
QA <- matrix(nrow = 1, ncol = 4,
dimnames = list(c("Control (conc = 0)"),
c("Number", "Mean", "Std. Dev.", "% Std. Dev")))
}
numberOfControls <- length(controls$response)
QA["Control (conc = 0)", 1] <- numberOfControls
if (numberOfControls > 0) {
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," ",
id," in database ",db,"\n")
}
exptypestring <- paste(toupper(substring(exptype,1,1)),
substring(exptype,2),sep="")
expdata$experimentator <- factor(expdata$experimentator)
expdata$type <- factor(expdata[[testtype]])
expdata$performed <- factor(as.character(expdata$performed))
expdata$substance <- factor(expdata$substance)
expdata$unit <- factor(expdata$unit)
expdata$ok <- factor(expdata$ok)
cat("\n",exptypestring,id,"from database",db,":\n\n",
"\tExperimentator(s):\t",levels(expdata$experimentator),"\n",
"\tType(s):\t\t",levels(expdata$type),"\n",
"\tPerformed on:\t\t",levels(expdata$performed),"\n",
"\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",levels(expdata$ok),"\n\n")
print(QA)
if (db == "ecotox") {
boxplot(controls$response,
names="controls",
ylab="Response",
ylim=c(0, max(controls$response, na.rm = TRUE)),
boxwex=0.4,
main=paste("Plate ",id))
} else {
boxplot(blinds$response,controls$response,
names=c("blinds","controls"),
ylab="Response",
boxwex=0.4,
main=paste("Plate ",id))
}
drdata <- expdata[c(2,4,6)]
drdata$substance <- factor(drdata$substance)
substances <- levels(drdata$substance)
lld <- log10(min(subset(drdata,conc!=0)$conc))
lhd <- log10(max(drdata$conc))
plot(1,type="n",
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)
for (i in 1:length(drdatalist)) {
points(log10(drdatalist[[i]]$conc),drdatalist[[i]][[responsename]],col=i);
}
legend("topright",substances, pch=1, col=1:length(substances), inset=0.05)
title(main=paste(levels(expdata$experimentator),
" - ",levels(expdata$type)))
}
|
