## ----setup, include = FALSE--------------------------------------------------- knitr::opts_chunk$set( fig.width = 8, fig.height = 8 ) ## ---- echo = FALSE,fig.asp=0.6------------------------------------------------ library(png) library(grid) path_intro <- system.file("extdata", "auto.png", package = "MACSQuantifyR") intro <- readPNG(path_intro) grid.raster(intro) ## ----load--------------------------------------------------------------------- library(MACSQuantifyR) library(knitr) library(grid) library(gridExtra) library(png) suppressMessages(library(R.utils)) ## ----load_file, include = TRUE------------------------------------------------ file <- system.file("extdata", "drugs.xlsx", package = "MACSQuantifyR") ## ----echo=FALSE--------------------------------------------------------------- print(basename(file)) ## ----echo=FALSE,include=FALSE------------------------------------------------- MACSQuant <- load_MACSQuant(file) my_data <- slot(MACSQuant, "my_data") ## ----echo=FALSE--------------------------------------------------------------- kable(head(my_data), digits = 4) ## ----eval=FALSE--------------------------------------------------------------- # MACSQuant <- pipeline(filepath = file, # sheet_name = NULL, # optional # number_of_replicates = 3, # number_of_conditions = 8, # control = T) ## ---- echo = FALSE------------------------------------------------------------ example_path <- system.file("extdata/", "plate_template_pipeline.png", package = "MACSQuantifyR") example_image <- readPNG(example_path) grid.raster(example_image) ## ----echo = FALSE------------------------------------------------------------- printf(paste("...To quit press ESC...\n", "...You can now select your conditions", "replicates (without control condition replicates)...\n", " --> 18 conditions:...1...2...3...4...5...6...7...8...OK\n", " --> Done: replicates identified\n", " --> Done: statistics on each condition replicates\n", "...You can now select your control replicates...\n", " --> 1 control: ...OK...\n", " --> Done: statistics on each control replicates\n", "--> Done: replicates stored in variable my_replicates_sorted\n", sep = " ")) ## ----echo = FALSE------------------------------------------------------------- warning(paste("In order_data(sorted_matrix_final, my_data, save.files =", "save.files) : \n !!! A2 not selected and will be ignored", sep = " ")) ## ---- echo=FALSE-------------------------------------------------------------- drugs_R_image <- system.file("extdata", "drugs.RDS", package = "MACSQuantifyR") MACSQuant <- readRDS(drugs_R_image) kable(slot(MACSQuant, "statistics"), digits = 4) ## ---- echo = FALSE, fig.width=20, fig.height=20,fig.asp=0.5------------------- example_res1 <- system.file("extdata/", "barplot_counts_pipeline.png", package = "MACSQuantifyR") example_res2 <- system.file("extdata/", "barplot_percent_pipeline.png", package = "MACSQuantifyR") img4 <- rasterGrob(as.raster(readPNG(example_res1)), interpolate = FALSE) img5 <- rasterGrob(as.raster(readPNG(example_res2)), interpolate = FALSE) grid.arrange(img4, img5, ncol = 2)