## ----setup, include = FALSE--------------------------------------------------- knitr::opts_chunk$set( collapse = TRUE, fig.width = 7, fig.height = 4 ) ## ----------------------------------------------------------------------------- library(gridify) library(magrittr) library(ggplot2) ## ----------------------------------------------------------------------------- figures_data <- list( global = list( project = "My Project", indication = "My Indication", study = "My Study", cutoff = "Data Cut-off: YYYY-MM-DD", program = "program1.R", var1 = "mpg", note1 = "Note: Violin figure: compact display of continuous distribution; it is a blend of boxplot and density, the latter based on a Gaussian kernel estimator.", note2 = "Note: Placebo subjects switched to Study Drug at/after Week 16.", note3 = "Note: Total Study Drug includes subjects randomized to Placebo and to Study Drug.", note4 = "Note: N denotes the treatment population and n denotes the contributing population for the analysis for each treatment, parameter and visit" ), figures = list( figure1 = list( number = "1.1", title1 = "My title Group A", title2 = "My title 2", var2 = "wt" ), figure2 = list( number = "1.2", title1 = "My Title Group B", title2 = "My title 2", var2 = "cyl" ) ) ) ## ----eval = FALSE------------------------------------------------------------- # library(readxl) # # dat <- readxl::read_excel("PATH TO YOUR FILE") # figures <- lapply(seq_len(nrow(dat)), function(row) dat[row, ]) # # Optionally, you can add names to the elements of 'figures' so you won't have to subset by index later # names(figures) <- paste0("figure", seq_along(figures)) # # Alternatively, you can leave the 'dat' object as it is and loop through its rows, # # or with row names if available ## ----------------------------------------------------------------------------- generate_figure <- function(data, var1, var2) { ggplot2::ggplot(data, ggplot2::aes(x = !!as.name(var1), y = !!as.name(var2))) + ggplot2::geom_line() } ## ----------------------------------------------------------------------------- figures_list <- list() ## ----------------------------------------------------------------------------- COMPANY <- "My Company" STATUS <- "DRAFT" ## ----------------------------------------------------------------------------- for (figure_index in seq_along(figures_data$figures)) { figure_obj <- generate_figure(mtcars, figures_data$global$var1, figures_data$figures[[figure_index]]$var2) # Add text elements using `sprintf()` gridify_obj <- gridify( object = figure_obj, layout = pharma_layout_A4() ) %>% # Add STATIC text elements to the `gridify` object # You can define these values as variables at the top of your script set_cell("header_left_1", COMPANY) %>% set_cell("watermark", toupper(STATUS)) %>% set_cell("header_right_2", STATUS) %>% # Add VARIABLE text elements to the gridify object set_cell("header_left_2", sprintf("%s / %s", figures_data$global$project, figures_data$global$indication)) %>% set_cell("header_left_3", figures_data$global$study) %>% set_cell("header_right_3", sprintf("%s", figures_data$global$cutoff)) %>% set_cell("output_num", sprintf("Output %s", figures_data$figures[[figure_index]]$number)) %>% set_cell("title_1", figures_data$figures[[figure_index]]$title1) %>% set_cell("title_2", figures_data$figures[[figure_index]]$title2) %>% set_cell("note", paste(figures_data$global[c("note1", "note2", "note3", "note4")], collapse = "\n")) %>% set_cell("footer_left", sprintf("Program: %s, %s", figures_data$global$program, Sys.time())) %>% set_cell("footer_right", sprintf("Page %s of %s", figure_index, length(figures_data$figures))) figures_list[[figure_index]] <- gridify_obj } ## ----eval = FALSE------------------------------------------------------------- # if (!dir.exists("figures")) { # dir.create("figures") # } ## ----eval = FALSE------------------------------------------------------------- # export_to( # figures_list, # sprintf("./figures/test_Company_A4_layout_%s.pdf", seq_along(figures_list)) # ) ## ----eval = FALSE------------------------------------------------------------- # export_to( # figures_list, # "./figures/test_multi_Company_A4_layout.pdf" # ) ## ----------------------------------------------------------------------------- library(gt) ## ----------------------------------------------------------------------------- table_cols <- c("cyl", "vs", "am", "drat", "qsec") # Columns that appear in final output df <- mtcars[, table_cols] rows_per_page <- 10 # Use the helper function to split the table pages <- paginate_table( df, rows_per_page = rows_per_page, fill_empty = " " # Optional: fills last page with a string for consistent positioning ) number_of_pages <- length(pages) ## ----fig.width=7.2, fig.height=7---------------------------------------------- # Define styling parameters row_height_pixels <- 10 font_size <- 12 font_type <- "serif" results_list <- list() for (iter in seq_along(pages)) { gt_input <- gt(pages[[iter]]) %>% tab_options( table.width = pct(80), data_row.padding = px(row_height_pixels), page.numbering = TRUE, table.font.size = font_size, table.font.names = font_type ) results_list[[iter]] <- gridify( gt_input, layout = pharma_layout_A4(global_gpar = grid::gpar(fontfamily = font_type)) ) %>% set_cell("header_left_1", "My Company") %>% set_cell("header_left_2", " / ") %>% set_cell("header_left_3", "") %>% set_cell("header_right_1", "CONFIDENTIAL") %>% set_cell("header_right_2", "") %>% set_cell("header_right_3", "Data Cut-off: YYYY-MM-DD") %>% set_cell("output_num", " xx.xx.xx") %>% set_cell("title_1", "") %>% set_cell("title_2", "<Title 2>") %>% set_cell("title_3", "<Optional Title 3>") %>% set_cell("note", "<Note or Footnotes>") %>% set_cell("references", "<References:>") %>% set_cell("footer_left", "Program: <PROGRAM NAME>, YYYY-MM-DD at HH:MM") %>% set_cell("footer_right", paste0("Page ", iter, " of ", number_of_pages)) %>% set_cell("watermark", "DRAFT") } print(results_list[[1]]) ## ----eval = FALSE------------------------------------------------------------- # if (!dir.exists("tables")) { # dir.create("tables") # } ## ----eval = FALSE------------------------------------------------------------- # export_to( # results_list, # to = "./tables/multipageA4.pdf" # ) # # export_to( # results_list, # to = "./tables/multipageA4portrait.pdf", # width = 8.3, # height = 11.7 # ) ## ----eval = FALSE------------------------------------------------------------- # export_to( # results_list[[1]], # to = "./tables/singlepage.png", # width = 2400, # height = 2000, # res = 300 # ) # # export_to( # results_list[[1]], # to = "./tables/singlepage.jpg", # width = 2400, # height = 2000, # res = 300 # ) ## ----eval = FALSE------------------------------------------------------------- # export_to( # results_list, # to = file.path("./tables", sprintf("singlepage%s.png", seq_along(results_list))), # width = 2400, # height = 2000, # res = 300 # ) # # export_to( # results_list, # to = file.path("./tables", sprintf("singlepage%s.jpg", seq_along(results_list))), # width = 2400, # height = 2000, # res = 300 # ) # # export_to( # results_list, # to = file.path("./tables", sprintf("singlepage%s.pdf", seq_along(results_list))), # width = 2400, # height = 2000, # res = 300 # ) ## ----fig.width = 7.2, fig.height = 45----------------------------------------- gt_obj <- gt::gt(Theoph) g <- gridify( object = gt_obj, layout = pharma_layout_letter() ) %>% set_cell("header_left_1", "My Company") %>% set_cell("header_left_2", "<PROJECT> / <INDICATION>") %>% set_cell("header_left_3", "<STUDY>") %>% set_cell("header_right_2", "<Draft or Final>") %>% set_cell("output_num", "<Table> xx.xx.xx") %>% set_cell("title_1", "<Title 1>") %>% set_cell("title_2", "<Title 2>") %>% set_cell("note", "<Note or Footnotes>") %>% set_cell("references", "<References:>") %>% set_cell("footer_left", "Program: <PROGRAM NAME>, YYYY-MM-DD at HH:MM") %>% set_cell("footer_right", "Page xx of nn") print(g)