targetplot: Dose-reponse plot for target items

View source: R/targetplot.R

targetplotR Documentation

Dose-reponse plot for target items


Plots dose-response raw data of target items (whether or not their response is considered significant) with fitted curves if available.


targetplot(items, f, = TRUE, dose_log_transfo = TRUE)



A character vector specifying the identifiers of the items to plot.


An object of class "drcfit".

If TRUE the fitted curve is added for items which were selected as responsive items and for which a best fit model was obtained.


If TRUE, default choice, a log transformation is used on the dose axis.


a ggplot object.


Marie-Laure Delignette-Muller

See Also

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", 

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, = FALSE)

aursiber/DRomics documentation built on June 19, 2024, 5:48 p.m.