## ----setup, include = FALSE--------------------------------------------------- knitr::opts_chunk$set( fig.width = 8, fig.height = 8 ) ## ---- echo = FALSE, fig.width=10, fig.height=8,fig.asp=0.6-------------------- library(png) library(grid) path_intro <- system.file("extdata", "manual.png", package = "MACSQuantifyR") intro <- readPNG(path_intro) grid.raster(intro) ## ---- echo = FALSE------------------------------------------------------------ path_img1 <- system.file("extdata", "combo.png", package = "MACSQuantifyR") img1 <- readPNG(path_img1) grid.raster(img1) ## ----load--------------------------------------------------------------------- library(MACSQuantifyR) library(knitr) library(grid) library(gridExtra) library(ggplot2) library(tools) library(readxl) library(lattice) library(latticeExtra) suppressMessages(library(R.utils)) ## ----------------------------------------------------------------------------- MACSQuant <- new_class_MQ(path = "output_path") ## ----------------------------------------------------------------------------- slot(MACSQuant, "experiment_name") <- "Combo drug1-drug2 HC line 101" ## ----load_file, include = TRUE------------------------------------------------ filepath <- system.file("extdata", "drugs.xlsx", package = "MACSQuantifyR") MACSQuant <- load_MACSQuant(filepath, sheet_name = "combo_drugs", MACSQuant.obj = MACSQuant) ## ----------------------------------------------------------------------------- # this line is used to created c_names variable # for this experiment according to selection slot(MACSQuant, "param.experiment")$c_names <- c(sprintf("Drug1_c%d", 1:4), # DRUG1 ALONE sprintf("Drug2_c%d", 1:3), # DRUG2 ALONE sprintf("D2[1]_D1[%d]", 1:4), # DRUG2_C1 + DRUG1_Cs sprintf("D2[2]_D1[%d]", 1:4), # DRUG2_C2 + DRUG1_Cs sprintf("D2[3]_D1[%d]", 1:4)) # DRUG2_C3 + DRUG1_Cs # custom colors can be defined (with control if selected) plt.col <- c(heat.colors(length(slot(MACSQuant, "param.experiment")$c_names)), 1) # dose vector of concentration each condition slot(MACSQuant, "param.experiment")$doses <- c(1, 3, 5, 10, # DRUG1 ALONE 0, 0, 0, # DRUG2 ALONE 1, 3, 5, 10, # DRUG2_C1 ++ DRUG1_Cs 1, 3, 5, 10, # DRUG2_C2 + DRUG1_Cs 1, 3, 5, 10 # DRUG2_C3 + DRUG1_Cs ) slot(MACSQuant, "param.experiment")$doses.alt <- c(0, 0, 0, 0, # DRUG1 ALONE 10, 50, 100, # DRUG2 ALONE 10, 10, 10, 10, # DRUG2_C1 + DRUG1_Cs 50, 50, 50, 50, # DRUG2_C2 ++ DRUG1_Cs 100, 100, 100, 100 # DRUG2_C3 ++ DRUG1_Cs ) ## ----eval=FALSE--------------------------------------------------------------- # # MACSQuant <- on_plate_selection(MACSQuant, # number_of_replicates = 3, # number_of_conditions = 19, # control = TRUE, # save.files = TRUE) ## ----include=F---------------------------------------------------------------- filepath <- system.file("extdata", "drugs.Rdata", package = "MACSQuantifyR") load(filepath) ## ----------------------------------------------------------------------------- plt.col <- c( heat.colors(length(slot(MACSQuant, "param.experiment")$c_names)), 1) plt.labels <- c(slot(MACSQuant, "param.experiment")$c_names, "Control") slot(MACSQuant, "param.output")$plt.title <- "Custom title example" ## ----fig.width=31.75, fig.height=15.875,fig.asp=0.5,fig.asp=0.5-------------- flav <- "counts" p_counts <- barplot_data(MACSQuant, plt.col = plt.col, plt.flavour = flav, plt.labels = plt.labels, plt.combo = TRUE, xlab = "Drug1", ylab = "Drug2") grid.arrange(p_counts) flav <- "percent" p_percent <- barplot_data(MACSQuant, plt.col = plt.col, plt.flavour = flav, plt.labels = plt.labels, plt.combo = TRUE, xlab = "Drug1", ylab = "Drug2") grid.arrange(p_percent) ## ----eval =FALSE-------------------------------------------------------------- # # flav='counts' # ggsave(paste(MACSQuant@param.output$path, # "/outputMQ/barplot_", flav, ".png", sep = ""), # width = 31.75, height = 15.875, # units = "cm", p_counts) # # flav='percent' # ggsave(paste(MACSQuant@param.output$path, # "/outputMQ/barplot_", flav, ".png", sep = ""), # width = 31.75, height = 15.875, # units = "cm", p_percent) ## ----------------------------------------------------------------------------- MACSQuant <- combination_index(MACSQuant) ## ----eval=FALSE--------------------------------------------------------------- # generate_report(MACSQuant)