save_plot_pdf: save plots in pdf

In toxplot: Batch Processing, Modeling and Visualizing the Dose-Response of High-Throughput Screening Bioassay

Description

save ggplot2 plots generated in a list to a pdf file

Usage

save_plot_pdf(plot_list, filename)

Arguments

plot_list	the r list object contains all ggplot2 objects
filename	the output file name, including the file directory

Examples

## start from raw data
# define assay
assay_info <- list(prim_assay = "Primary",toxi_assay = "Cytotox")
# data normalization
demo_mc_norm <- normalize_per_plate(demo_mc, nctrl = "DMSO")
# filter out two test chemicals
demo_mc_norm <- dplyr::filter(demo_mc_norm, spid %in% c("TP0001502B05", "TP0001502B01"))
# fit curve with default 20% threshold
demo_md <- fit_curve_tcpl(demo_mc_norm, assay_info)
# calculate TAA and Med_diff only
demo_rank <- rank_tcpl(demo_md, med_taa = NULL, med_med_diff = NULL)
#produce plots with notations
demo_plots <- plot_tcpl_minimal(demo_md, demo_rank, notation = TRUE)

## save all the plots as pdf
# save_plot_pdf(demo_plots, ".\output plots\all_plots.pdf")

## save the 1st plot as pdf
# save_plot_pdf(demo_plots[1], ".\output plots\plot1.pdf")

toxplot documentation built on April 3, 2018, 9:04 a.m.