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
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
|
if(getRversion() >= '2.15.1') utils::globalVariables(c("dose", "Substance", "mtype"))
drplot <- function(drresults, data,
dtype = "std", alpha = 0.95, ctype = "none",
path = "./", fileprefix = "drplot", overlay = FALSE,
xlim = c("auto","auto"), ylim = c("auto","auto"),
xlab = paste("Decadic Logarithm of the dose in ", unit),
ylab = "Normalized response",
axes = TRUE, frame.plot = TRUE,
postscript = FALSE, pdf = FALSE, png = FALSE,
bw = TRUE,
pointsize = 12,
colors = 1:8, ltys = 1:8, pchs = "auto",
devoff=TRUE, lpos="topright")
{
# Check if all data have the same unit
unitlevels <- levels(as.factor(drresults$unit))
if (length(unitlevels) == 1) {
unit <- unitlevels
} else {
unit <- "different units"
}
# Determine the plot limits on the x-axis and y axis
if(is.data.frame(data)) {
# Get rid of pseudo substance names of controls
nonzerodata <- subset(data,dose!=0)
nonzerodata$substance <- factor(nonzerodata$substance)
zerodata <- subset(data,dose==0)
nc <- length(zerodata$dose) # Number of control points
if (nc > 0) {
sdc <- sd(zerodata$response)
controlconf <- sdc * qt((1 + alpha)/2, nc - 1) / sqrt(nc)
if (nc < 3) {
ctype = "none"
}
} else {
if (ctype != "none") {
stop("There are no controls in the dataset, and therefore ",
"their scatter cannot be displayed\n")
}
}
lld <- log10(min(nonzerodata$dose))
lhd <- log10(max(nonzerodata$dose))
hr <- max(nonzerodata$response)
if (ctype == "std") hr <- max(hr,1 + sdc)
if (ctype == "conf") hr <- max(hr,1 + controlconf)
dsubstances <- levels(nonzerodata$substance)
} else {
lld <- min(drresults[["logED50"]],na.rm=TRUE) - 2
lhd <- max(drresults[["logED50"]],na.rm=TRUE) + 2
if (length(subset(drresults,mtype=="linlogit")$Substance) != 0) {
hr <- 1.8
} else {
hr <- 1.0
}
}
if (xlim[1] == "auto") xlim[1] <- lld - 0.5
if (xlim[2] == "auto") xlim[2] <- lhd + 1
if (ylim[1] == "auto") ylim[1] <- -0.1
if (ylim[2] == "auto") ylim[2] <- hr + 0.2
xlim <- as.numeric(xlim)
ylim <- as.numeric(ylim)
# Prepare overlay plot if requested
if (overlay)
{
if (pchs == "auto") pchs = 1:length(dsubstances)
if (postscript) {
filename = paste(path,fileprefix,".eps",sep="")
postscript(file=filename,
paper="special",width=7,height=7,horizontal=FALSE, pointsize=pointsize)
message("Created File: ",filename,"\n")
}
if (pdf) {
filename = paste(path,fileprefix,".pdf",sep="")
pdf(file=filename,
paper="special",width=7,height=7,horizontal=FALSE, pointsize=pointsize)
message("Created File: ",filename,"\n")
}
if (png) {
filename = paste(path,fileprefix,".png",sep="")
png(filename=filename,
width=500, height=500, pointsize=pointsize)
message("Created File: ",filename,"\n")
}
plot(0,type="n",
xlim = xlim,
ylim = ylim,
xlab = xlab,
ylab = ylab,
axes = axes,
frame.plot = frame.plot)
} else {
# If overlay plot is not requested, ask before showing multiple plots on the screen
if (pchs == "auto") pchs = rep(1, length(dsubstances))
if (!postscript && !png && !pdf && length(dsubstances) > 1) {
op <- par(ask=TRUE)
on.exit(par(op))
}
}
# nl is the overall number of fits to draw by different line types
nl <- 0
# Plot the data either as raw data or as error bars
if(is.data.frame(data)) {
splitted <- split(nonzerodata,nonzerodata$substance)
# n is the index for the dose-response curves
n <- 0
if (bw) colors <- rep("black",length(dsubstances))
# Loop over the substances in the data (index n)
for (i in dsubstances) {
n <- n + 1
tmp <- splitted[[i]]
if (length(tmp$response) != 0) {
color <- colors[[n]]
pch <- pchs[[n]]
# Prepare the single graphs if an overlay is not requested
if (!overlay)
{
if (postscript) {
filename = paste(path,fileprefix,sub(" ","_",i),".eps",sep="")
postscript(file=filename,
paper="special",width=7,height=7,horizontal=FALSE,pointsize=pointsize)
message("Created File: ",filename,"\n")
}
if (pdf) {
filename = paste(path,fileprefix,sub(" ","_",i),".pdf",sep="")
pdf(file=filename,
paper="special",width=7,height=7,horizontal=FALSE,pointsize=pointsize)
message("Created File: ",filename,"\n")
}
if (png) {
filename = paste(path,fileprefix,sub(" ","_",i),".png",sep="")
png(filename=filename,
width=500, height=500, pointsize=pointsize)
message("Created File: ",filename,"\n")
}
plot(0,type="n",
xlim = xlim,
ylim = ylim,
xlab = xlab,
ylab = ylab,
axes = axes,
frame.plot = frame.plot)
}
if (!overlay) legend(lpos, i, lty = 1, col = color, pch = pch, inset=0.05)
tmp$dosefactor <- factor(tmp$dose) # necessary because the old
# factor has all levels, not
# only the ones tested with
# this substance
# Plot the control lines, if requested
if (ctype == "std") {
abline(h = 1 - sdc, lty = 2)
abline(h = 1 + sdc, lty = 2)
}
if (ctype == "conf") {
abline(h = 1 - controlconf, lty = 2)
abline(h = 1 + controlconf, lty = 2)
}
# Plot the data, if requested
if (dtype != "none") {
if (dtype == "raw") {
points(log10(tmp$dose), tmp$response, col = color, pch = pch)
} else {
splitresponses <- split(tmp$response,tmp$dosefactor)
means <- sapply(splitresponses,mean)
lengths <- sapply(splitresponses,length)
vars <- sapply(splitresponses,var)
standarddeviations <- sqrt(vars)
}
if (dtype == "std")
{
tops <- means + standarddeviations
bottoms <- means - standarddeviations
}
if (dtype == "conf")
{
confidencedeltas <- qt((1 + alpha)/2, lengths - 1) * sqrt(vars)
tops <- means + confidencedeltas
bottoms <- means - confidencedeltas
}
if (dtype != "raw")
{
x <- log10(as.numeric(levels(tmp$dosefactor)))
segments(x,bottoms,x,tops,col=color)
points(x, means, col = color, pch = pch)
smidge <- 0.05
segments(x - smidge,bottoms,x + smidge,bottoms,col=color)
segments(x - smidge,tops,x + smidge,tops,col=color)
}
}
# Plot the fits for this substance, if there are any
fits <- subset(drresults,Substance == i)
fit.rows <- rownames(fits)
nf <- length(fit.rows) # number of fits to plot for this substance
if (nf > 0) {
for (j in 1:nf)
{
fit.row = fit.rows[j]
if (overlay) nl <- nl + 1 else nl = j
lty <- ltys[nl]
if (drresults[[fit.row, "mtype"]] %in% c("probit",
"logit",
"weibull",
"linlogit"))
{
m <- attr(drresults, "models")[[as.numeric(fit.row)]]
of <- function(x) {
predict(m, data.frame(dose = 10^x))
}
plot(of, lld - 0.5, lhd + 2,
add = TRUE, col = color, lty = lty)
}
}
}
if (!overlay && (postscript || png || pdf)) dev.off()
} else {
message("No data for ",i,"\n")
}
}
}
if (overlay) legend(lpos, dsubstances, col = colors, pch = pchs, lty = ltys, inset=0.05)
if (overlay && (postscript || png || pdf)) {
if (devoff) {
dev.off()
}
}
}
|
