targetplot: Dose-reponse plot for target items

In DRomics: Dose Response for Omics

Dose-reponse plot for target items

Description

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

Usage

targetplot(items, f, add.fit = TRUE, dose_log_transfo = TRUE)

Arguments

items	A character vector specifying the identifiers of the items to plot.
f	An object of class "drcfit".
add.fit	If TRUE the fitted curve is added for items which were selected as responsive items and for which a best fit model was obtained.
dose_log_transfo	If TRUE, default choice, a log transformation is used on the dose axis.

Value

a ggplot object.

Author(s)

Marie-Laure Delignette-Muller

See Also

See plot.drcfit.

Examples

# 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)

DRomics documentation built on Oct. 16, 2024, 5:09 p.m.