targetplot | R Documentation |
Plots dose-response raw data of target items (whether or not their response is considered significant) with fitted curves if available.
targetplot(items, f, add.fit = TRUE, dose_log_transfo = TRUE)
items |
A character vector specifying the identifiers of the items to plot. |
f |
An object of class |
add.fit |
If |
dose_log_transfo |
If |
a ggplot object.
Marie-Laure Delignette-Muller
See plot.drcfit
.
# A toy example on a very small subsample of a microarray data set)
#
datafilename <- system.file("extdata", "transcripto_very_small_sample.txt",
package="DRomics")
o <- microarraydata(datafilename, check = TRUE, norm.method = "cyclicloess")
s_quad <- itemselect(o, select.method = "quadratic", FDR = 0.01)
f <- drcfit(s_quad, progressbar = TRUE)
# Plot of chosen items with fitted curves when available
#
targetitems <- c("88.1", "1", "3", "15")
targetplot(targetitems, f = f)
# The same plot in raw scale instead of default log scale
#
targetplot(targetitems, f = f, dose_log_transfo = FALSE)
# The same plot in x log scale choosing x limits for plot
# to enlarge the space between the control and the non null doses
#
if (require(ggplot2))
targetplot(targetitems, f = f, dose_log_transfo = TRUE) +
scale_x_log10(limits = c(0.1, 10))
# The same plot without fitted curves
#
targetplot(targetitems, f = f, add.fit = FALSE)
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