Nothing
# Plot of fitted curves using columns of on extended dataframe to optionnally code
# for color and or facet
curvesplot <- function(extendedres, xmin = 0, xmax,
y0shift = TRUE, scaling = FALSE,
facetby, facetby2, free.y.scales = FALSE,
ncol4faceting, colorby, removelegend = FALSE,
npoints = 500, line.size = 0.2, line.alpha = 1,
dose_log_transfo = FALSE)
{
if (missing(extendedres) | !is.data.frame(extendedres))
stop("The first argument of curvesplot must be a dataframe
(see ?curvesplot for details).")
if(scaling & !y0shift)
{
y0shift <- TRUE
warning(strwrap(prefix = "\n", initial = "\n",
"y0shift is forced to TRUE when scaling is TRUE."))
}
cnames <- colnames(extendedres)
if (scaling)
{
if (any(!is.element(c("id", "model", "b", "c", "d", "e", "f", "y0", "maxychange"), cnames)))
stop("The first argument of curvesplot must be a dataframe
containing at least columns named id, model, b, c, d, e, f, y0 and maxychange.")
} else
{
if (any(!is.element(c("id", "model", "b", "c", "d", "e", "f", "y0"), cnames)))
stop("The first argument of curvesplot must be a dataframe
containing at least columns named id, model, b, c, d, e, f and y0.")
}
if (missing(xmax))
stop("xmax must be given. You can fix it at max(f$omicdata$dose)}
with f the output of drcfit().")
if (dose_log_transfo)
{
if (xmin == 0)
stop("When using a log scale for the dose, a strictly positive value must be given for xmin.")
x2plot <- 10^seq(log10(xmin), log10(xmax), length.out = npoints)
} else
{
x2plot <- seq(xmin, xmax, length.out = npoints)
}
ns <- nrow(extendedres)
N <- ns * npoints
if (free.y.scales)
{
scales.arg <- "free_y"
} else
{
scales.arg <- "fixed"
}
curves2plot <- data.frame(x = rep(x2plot, ns),
id = rep(extendedres$id, each = npoints),
y = numeric(length = N))
if (!missing(facetby))
{
if (!is.character(facetby))
stop("facetby should be a character string for the name of the column used for facetting.")
if (!is.element(facetby, cnames))
stop("facetby should be a character string corresponding to the name of a column of
extendedres, the dataframe given in input.")
curves2plot$facetby <- rep(extendedres[, facetby], each = npoints)
if (!missing(facetby2))
{
if (!is.character(facetby2))
stop("facetby2 should be a character string for the name of the column used for facetting.")
if (!is.element(facetby2, cnames))
stop("facetby2 should be a character string corresponding to the name of a column of
extendedres, the dataframe given in input.")
curves2plot$facetby2 <- rep(extendedres[, facetby2], each = npoints)
}
}
if (!missing(colorby))
{
if (!is.character(colorby))
stop("colorby should be a character string for the name of the column coding for the point color.")
if (!is.element(colorby, cnames))
stop("colorby should be a character string corresponding to the name of a column of
extendedres, the dataframe given in input.")
}
for (i in 1:ns)
{
modeli <- extendedres$model[i]
if (modeli == "linear")
{
b <- extendedres$b[i]
d <- extendedres$d[i]
curves2plot$y[(i-1)*npoints + 1:npoints] <- flin(x2plot, b = extendedres$b[i],
d = extendedres$d[i])
} else
if (modeli == "exponential")
{
curves2plot$y[(i-1)*npoints + 1:npoints] <- fExpo(x2plot, b = extendedres$b[i],
d = extendedres$d[i], e = extendedres$e[i])
} else
if (modeli == "Hill")
{
curves2plot$y[(i-1)*npoints + 1:npoints] <- fHill(x2plot, b = extendedres$b[i], c = extendedres$c[i],
d = extendedres$d[i], e = extendedres$e[i])
} else
if (modeli == "Gauss-probit")
{
curves2plot$y[(i-1)*npoints + 1:npoints] <- fGauss5p(x2plot, b = extendedres$b[i], c = extendedres$c[i],
d = extendedres$d[i], e = extendedres$e[i],
f = extendedres$f[i])
} else
if (modeli == "log-Gauss-probit")
{
curves2plot$y[(i-1)*npoints + 1:npoints] <- fLGauss5p(x2plot, b = extendedres$b[i], c = extendedres$c[i],
d = extendedres$d[i], e = extendedres$e[i],
f = extendedres$f[i])
}
if (y0shift)
{
if (scaling)
{
curves2plot$y[(i-1)*npoints + 1:npoints] <-
(curves2plot$y[(i-1)*npoints + 1:npoints] - extendedres$y0[i]) / extendedres$maxychange[i]
} else
{
curves2plot$y[(i-1)*npoints + 1:npoints] <-
curves2plot$y[(i-1)*npoints + 1:npoints] - extendedres$y0[i]
}
}
}
# no color no facet
if (missing(colorby) & missing(facetby))
{
gg <- ggplot(data = curves2plot, mapping = aes_(x = quote(x), y = quote(y), group = quote(id))) +
geom_line(size = line.size, alpha = line.alpha)
} else
# facet only
if (missing(colorby))
{
curves2plot$facetby <- rep(extendedres[, facetby], each = npoints)
gg <- ggplot(data = curves2plot, mapping = aes_(x = quote(x), y = quote(y), group = quote(id))) +
geom_line(size = line.size, alpha = line.alpha)
# +
# facet_wrap(~ facetby, scales = scales.arg)
} else
# color only
if (missing(facetby))
{
curves2plot$colorby <- rep(extendedres[, colorby], each = npoints)
gg <- ggplot(data = curves2plot, mapping = aes_(x = quote(x), y = quote(y), group = quote(id), colour = quote(colorby))) +
geom_line(size = line.size, alpha = line.alpha)
} else
# color and facet
{
curves2plot$facetby <- rep(extendedres[, facetby], each = npoints)
curves2plot$colorby <- rep(extendedres[, colorby], each = npoints)
gg <- ggplot(data = curves2plot, mapping = aes_(x = quote(x), y = quote(y), group = quote(id), colour = quote(colorby))) +
geom_line(size = line.size, alpha = line.alpha)
}
if (!missing(facetby))
{
if (!missing(facetby2))
{
gg <- gg + facet_grid(facetby2 ~ facetby, scales = scales.arg)
}
else
{
if (missing(ncol4faceting))
{
gg <- gg + facet_wrap(~ facetby, scales = scales.arg)
} else
{
gg <- gg + facet_wrap(~ facetby, scales = scales.arg, ncol = ncol4faceting)
}
}
}
if (removelegend) gg <- gg + theme(legend.position = "none")
if (dose_log_transfo)
gg <- gg + scale_x_log10()
return(gg)
}
Any scripts or data that you put into this service are public.
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.