updated instruction templates

bin/induction-instructions.R

@@ -0,0 +1,91 @@
+#!/usr/bin/env Rscript
+
+library(rjson)
+library(gridExtra)
+library(grid)
+library(png)
+
+insert_overview <- function(data, x_margin, y_initial, y_spacing, font_size) {
+  grid.text("Induction of protein expression in OT-2", x = x_margin, y = y_initial, just = "left", gp = gpar(fontsize = font_size + 4, fontface = "bold"))
+  overview <- c("Quick Overview",
+                paste("Once the cultures have reached the desired growth phase, the robot transfers cells to appropriate plates."),
+                paste("The robot adds an inducer to the cultures."),
+                paste("After induction, cultures are incubated to allow for protein expression."))
+  overview_y_lines <- (y_initial - 2*y_spacing) - seq(0, length(overview) - 1) * y_spacing
+  text_style <- gpar(fontsize = font_size, fontface = c("bold", rep("plain", length(overview) - 1)))
+  grid.text(overview, x = x_margin, y = overview_y_lines, just = "left", gp = text_style)
+  return(overview_y_lines[length(overview_y_lines)]-y_spacing)
+}
+
+insert_preparation <- function(x_margin, y_initial, y_spacing) {
+  preparation <- c("Preparation",
+                   "Prepare the reagents and labware according to the below diagrams.",
+                   "Volumes (uL) indicate how much of reagents will be used, so add additional volume.")
+
+  preparation_y_lines <- y_initial - y_spacing * (1:length(preparation))
+  text_style <- gpar(fontsize = 12, fontface = c("bold", rep("plain", length(preparation) - 1)))
+  grid.text(preparation, x = x_margin, y = preparation_y_lines, just = "left", gp = text_style)
+  return(preparation_y_lines[length(preparation_y_lines)]-y_spacing)
+}
+
+insert_labware <- function(visualised_labware, width, height, x_margin, y_initial, y_spacing) {
+  image_files <- list.files(visualised_labware, pattern = "^0", full.names = TRUE)
+  num_images <- length(image_files)
+
+  positions <- list()
+  # Generate positions
+  for (i in 1:num_images) {
+    # Calculate position based on index
+    x <- x_margin + width/2 + ((i - 1) %% 2) * width
+    y <- y_initial - height/2 + floor((i - 1) / 2) * - height
+    positions[[i]] <- list(x = x, y = y)
+  }
+    # Insert each image into the PDF
+  for (i in seq_along(image_files)) {
+    if (file.exists(image_files[i])) {
+      image <- readPNG(image_files[i])
+      position <- positions[[i]]
+      grid.raster(image, x = position$x, y = position$y, width = width, height = height)
+    }
+  }
+
+  return(positions[[num_images]]$y - height/2 - y_spacing)
+}
+
+insert_deck_loading <- function(data, x_margin, y_initial, font_size, y_spacing) {
+  deck <- c("Deck Loading Instructions",
+                paste("Check that", data$right_pipette_name, "is in the right mount, and", data$left_pipette_name, "is in the left mount." ),
+                paste("Slot", paste(data$right_pipette_tiprack_slot, collapse = ", "), ": load", data$right_pipette_tiprack_name, "for the", data$right_pipette_name, "pipette."),
+                paste("Slot", paste(data$left_pipette_tiprack_slot, collapse = ", "), ": load", data$left_pipette_tiprack_name, "for the", data$left_pipette_name, "pipette."),
+                paste("Slot", data$blank_plate_slot, ": load", data$blank_plate_name, "containing blank for the plate reader."),
+                paste("Slot", data$culture_plate_slot, ": load", data$culture_plate_name, "containing the cell culture."),
+                paste("Slot", data$inducer_plate_slot, ": load", data$inducer_plate_name, "containing the inducer."),
+                paste("Slot", data$destination_plate_slot, ": load", data$destination_plate_name, " where the induction occurs."))
+  deck_y_lines <- y_initial - seq(0, length(deck) - 1) * y_spacing
+  text_style <- gpar(fontsize = font_size, fontface = c("bold", rep("plain", length(deck) - 1)))
+  grid.text(deck, x = x_margin, y = deck_y_lines, just = "left", gp = text_style)
+}
+
+instructions <- function(json_file_path, visualised_labware, output_file, x_margin = 0.05, y_spacing = 0.02, labware_width = 0.45, labware_height = 0.27, font_size = 12, y_initial = 0.98) {
+  pdf(output_file, width = 8.5, height = 11)
+  par(mar = c(5, 4, 4, 2) + 0.1)
+  json_data <- fromJSON(file = json_file_path)
+
+  overview <- insert_overview(json_data, x_margin, y_initial, y_spacing, font_size) # Title and Overview
+  preparation <- insert_preparation(x_margin, overview, y_spacing)   # Reagents preparation
+
+  labware <- insert_labware(visualised_labware, labware_width, labware_height, x_margin, preparation, y_spacing)   # # Insert images and get coordinates
+  deck_loading <- insert_deck_loading(json_data, x_margin, labware, font_size, y_spacing)
+
+  dev.off()
+
+}
+
+# Command-line arguments
+args <- commandArgs(trailingOnly = TRUE)
+json_file_path <- args[1]
+visualised_labware <- args[2]
+output_file <- args[3]
+
+# Generateinstructions
+instructions(json_file_path, visualised_labware, output_file)

bin/picking-instructions.R

@@ -0,0 +1,91 @@
+#!/usr/bin/env Rscript
+
+library(rjson)
+library(gridExtra)
+library(grid)
+library(png)
+
+insert_overview <- function(data, x_margin, y_initial, y_spacing, font_size) {
+  grid.text("Colony picking in OT-2", x = x_margin, y = y_initial, just = "left", gp = gpar(fontsize = font_size + 4, fontface = "bold"))
+  overview <- c("Quick Overview",
+                paste("The colonies were picked using a pipette tip and transferred to destination plate containing fresh media."),
+                paste("The plate is then incubated under the required conditions for further growth."),
+                paste("The robot picked colonies from total of", length(data$agar_plate_slot), "agar plates."),
+                paste("The picking height into the agar is set at ", data$agar_stab_depth, "mm."),
+                paste("The agar height is calculated automatically per plate based on:"),
+                paste("its shape (", data$agar_plate_shape, ") and dimensions (", paste(data$agar_plate_dimensions, collapse=", "), "in mm),"),
+                paste("the plate weight without agar (", data$plate_weight_without_agar, "g) and with agar (g),"),
+                paste("and agar density of ", data$agar_density,"(g/mm3)."))
+  overview_y_lines <- (y_initial - 2*y_spacing) - seq(0, length(overview) - 1) * y_spacing
+  text_style <- gpar(fontsize = font_size, fontface = c("bold", rep("plain", length(overview) - 1)))
+  grid.text(overview, x = x_margin, y = overview_y_lines, just = "left", gp = text_style)
+  return(overview_y_lines[length(overview_y_lines)]-y_spacing)
+}
+insert_preparation <- function(x_margin, y_initial, y_spacing) {
+  preparation <- c("Preparation",
+                   "The colonies are picked in accordance to the plate layout below.")
+  preparation_y_lines <- y_initial - y_spacing * (1:length(preparation))
+  text_style <- gpar(fontsize = 12, fontface = c("bold", rep("plain", length(preparation) - 1)))
+  grid.text(preparation, x = x_margin, y = preparation_y_lines, just = "left", gp = text_style)
+  return(preparation_y_lines[length(preparation_y_lines)]-y_spacing)
+}
+
+insert_labware <- function(visualised_labware, width, height, x_margin, y_initial, y_spacing) {
+  image_files <- list.files(visualised_labware, pattern = "^0", full.names = TRUE)
+  num_images <- length(image_files)
+
+  positions <- list()
+  # Generate positions
+  for (i in 1:num_images) {
+    # Calculate position based on index
+    x <- x_margin + width/2 + ((i - 1) %% 2) * width
+    y <- y_initial - height/2 + floor((i - 1) / 2) * - height
+    positions[[i]] <- list(x = x, y = y)
+  }
+    # Insert each image into the PDF
+  for (i in seq_along(image_files)) {
+    if (file.exists(image_files[i])) {
+      image <- readPNG(image_files[i])
+      position <- positions[[i]]
+      grid.raster(image, x = position$x, y = position$y, width = width, height = height)
+    }
+  }
+
+  return(positions[[num_images]]$y - height/2 - y_spacing)
+}
+
+insert_deck_loading <- function(data, x_margin, y_initial, font_size, y_spacing) {
+  deck <- c("Deck Loading Instructions",
+                paste("Check that", data$pipette_name, "is in the", data$pipette_mount, "mount"),
+                paste("Slot", paste(data$pipette_tiprack_slot, collapse = ", "), ": load", data$pipette_tiprack_name, "for the", data$pipette_name, "pipette."),
+                paste("Slot", data$agar_plate_slot, ": load", data$agar_plate_name, "with agar."),
+                paste("Slot", data$media_plate_slot, ": load", data$media_plate_name, "containing fresh media."))
+  deck_y_lines <- y_initial - seq(0, length(deck) - 1) * y_spacing
+  text_style <- gpar(fontsize = font_size, fontface = c("bold", rep("plain", length(deck) - 1)))
+  grid.text(deck, x = x_margin, y = deck_y_lines, just = "left", gp = text_style)
+}
+
+instructions <- function(json_file_path, visualised_labware, output_file, x_margin = 0.05, y_spacing = 0.02, labware_width = 0.45, labware_height = 0.27, font_size = 12, y_initial = 0.98) {
+  pdf(output_file, width = 8.5, height = 11)
+  par(mar = c(5, 4, 4, 2) + 0.1)
+  json_data <- fromJSON(file = json_file_path)
+
+  overview <- insert_overview(json_data, x_margin, y_initial, y_spacing, font_size) # Title and Overview
+  preparation <- insert_preparation(x_margin, overview, y_spacing)   # Reagents preparation
+
+
+  labware <- insert_labware(visualised_labware, labware_width, labware_height, x_margin, preparation, y_spacing)   # # Insert images and get coordinates
+  deck_loading <- insert_deck_loading(json_data, x_margin, labware, font_size, y_spacing)
+
+  dev.off()
+
+}
+
+# Command-line arguments
+args <- commandArgs(trailingOnly = TRUE)
+json_file_path <- args[1]
+visualised_labware <- args[2]
+output_file <- args[3]
+
+# Generateinstructions
+instructions(json_file_path, visualised_labware, output_file)

bin/spotting-instructions.R

@@ -0,0 +1,96 @@
+#!/usr/bin/env Rscript
+
+library(rjson)
+library(gridExtra)
+library(grid)
+library(png)
+
+insert_overview <- function(data, x_margin, y_initial, y_spacing, font_size) {
+  grid.text("Spotting in OT-2", x = x_margin, y = y_initial, just = "left", gp = gpar(fontsize = font_size + 4, fontface = "bold"))
+  overview <- c("Quick Overview",
+                paste("The robot spots transformed cells on the total of", length(data$agar_plate_slot), "agar plates."),
+                paste("The pipette aspirates additional", data$dead_volume, "uL of transfromed cells."),
+                paste("The spotting height above the agar is set at ", data$spotting_height, "mm."),
+                paste("The agar height is calculated automatically per plate based on:"),
+                paste("its shape (", data$agar_plate_shape, ") and dimensions (", paste(data$agar_plate_dimensions, collapse=", "), "in mm),"),
+                paste("the plate weight without agar (", data$plate_weight_without_agar, "g) and with agar (g),"),
+                paste("and agar density of ", data$agar_density,"(g/mm3)."))
+  overview_y_lines <- (y_initial - 2*y_spacing) - seq(0, length(overview) - 1) * y_spacing
+  text_style <- gpar(fontsize = font_size, fontface = c("bold", rep("plain", length(overview) - 1)))
+  grid.text(overview, x = x_margin, y = overview_y_lines, just = "left", gp = text_style)
+  return(overview_y_lines[length(overview_y_lines)]-y_spacing)
+}
+insert_preparation <- function(x_margin, y_initial, y_spacing) {
+  preparation <- c("Preparation",
+                   "The plates are spotted in uL according to the layout below.")
+  preparation_y_lines <- y_initial - y_spacing * (1:length(preparation))
+  text_style <- gpar(fontsize = 12, fontface = c("bold", rep("plain", length(preparation) - 1)))
+  grid.text(preparation, x = x_margin, y = preparation_y_lines, just = "left", gp = text_style)
+  return(preparation_y_lines[length(preparation_y_lines)]-y_spacing)
+}
+
+insert_labware <- function(visualised_labware, width, height, x_margin, y_initial, y_spacing) {
+  # List all files that start with a number, ensuring full names are returned
+  image_files <- list.files(visualised_labware, pattern = "^\\d+", full.names = TRUE)
+
+  # Sort the files numerically based on their prefix
+  image_files <- sort(image_files, method = "radix")
+
+  num_images <- length(image_files)
+
+  positions <- list()
+  # Generate positions
+  for (i in 1:num_images) {
+    # Calculate position based on index
+    x <- x_margin + width/2 + ((i - 1) %% 2) * width
+    y <- y_initial - height/2 - floor((i - 1) / 2) * height # Adjusted calculation
+    positions[[i]] <- list(x = x, y = y)
+  }
+
+  # Insert each image into the PDF
+  for (i in seq_along(image_files)) {
+    if (file.exists(image_files[i])) {
+      image <- readPNG(image_files[i])
+      position <- positions[[i]]
+      grid.raster(image, x = position$x, y = position$y, width = width, height = height)
+    }
+  }
+
+  return(positions[[num_images]]$y - height/2 - y_spacing)
+}
+
+insert_deck_loading <- function(data, x_margin, y_initial, font_size, y_spacing) {
+  deck <- c("Deck Loading Instructions",
+                paste("Check that", data$pipette_name, "is in the", data$pipette_mount,"mount."),
+                paste("Slot", paste(data$pipette_tiprack_slots, collapse = ", "), ": load", data$pipette_tiprack_name, "for the", data$pipette_name, "pipette."),
+                paste("Slot", data$agar_plate_slot, ": load", data$agar_plate_name, "with agar."),
+                paste("Slot", data$transformation_plate_slot, ": load", data$transformation_plate_name, "containing transformed cells."))
+  deck_y_lines <- y_initial - seq(0, length(deck) - 1) * y_spacing
+  text_style <- gpar(fontsize = font_size, fontface = c("bold", rep("plain", length(deck) - 1)))
+  grid.text(deck, x = x_margin, y = deck_y_lines, just = "left", gp = text_style)
+}
+
+instructions <- function(json_file_path, visualised_labware, output_file, x_margin = 0.05, y_spacing = 0.02, labware_width = 0.45, labware_height = 0.27, font_size = 12, y_initial = 0.98) {
+  pdf(output_file, width = 8.5, height = 11)
+  par(mar = c(5, 4, 4, 2) + 0.1)
+  json_data <- fromJSON(file = json_file_path)
+
+  overview <- insert_overview(json_data, x_margin, y_initial, y_spacing, font_size) # Title and Overview
+  preparation <- insert_preparation(x_margin, overview, y_spacing)   # Reagents preparation
+
+
+  labware <- insert_labware(visualised_labware, labware_width, labware_height, x_margin, preparation, y_spacing)   # # Insert images and get coordinates
+  deck_loading <- insert_deck_loading(json_data, x_margin, labware, font_size, y_spacing)
+
+  dev.off()
+
+}
+
+# Command-line arguments
+args <- commandArgs(trailingOnly = TRUE)
+json_file_path <- args[1]
+visualised_labware <- args[2]
+output_file <- args[3]
+
+# Generateinstructions
+instructions(json_file_path, visualised_labware, output_file)

bin/transfer-instructions.R

@@ -0,0 +1,84 @@
+#!/usr/bin/env Rscript
+
+library(rjson)
+library(gridExtra)
+library(grid)
+library(png)
+
+insert_overview <- function(data, x_margin, y_initial, y_spacing, font_size) {
+  grid.text("Simple liquid transfer in OT-2", x = x_margin, y = y_initial, just = "left", gp = gpar(fontsize = font_size + 4, fontface = "bold"))
+  overview <- c("Quick Overview",
+                paste("The transfer of liquids."))
+  overview_y_lines <- (y_initial - 2*y_spacing) - seq(0, length(overview) - 1) * y_spacing
+  text_style <- gpar(fontsize = font_size, fontface = c("bold", rep("plain", length(overview) - 1)))
+  grid.text(overview, x = x_margin, y = overview_y_lines, just = "left", gp = text_style)
+  return(overview_y_lines[length(overview_y_lines)]-y_spacing)
+}
+insert_preparation <- function(x_margin, y_initial, y_spacing) {
+  preparation <- c("Preparation",
+                   "The liquids are transferred according to the layout below (uL).")
+  preparation_y_lines <- y_initial - y_spacing * (1:length(preparation))
+  text_style <- gpar(fontsize = 12, fontface = c("bold", rep("plain", length(preparation) - 1)))
+  grid.text(preparation, x = x_margin, y = preparation_y_lines, just = "left", gp = text_style)
+  return(preparation_y_lines[length(preparation_y_lines)]-y_spacing)
+}
+
+insert_labware <- function(visualised_labware, width, height, x_margin, y_initial, y_spacing) {
+  image_files <- list.files(visualised_labware, pattern = "^0", full.names = TRUE)
+  num_images <- length(image_files)
+
+  positions <- list()
+  # Generate positions
+  for (i in 1:num_images) {
+    # Calculate position based on index
+    x <- x_margin + width/2 + ((i - 1) %% 2) * width
+    y <- y_initial - height/2 + floor((i - 1) / 2) * - height
+    positions[[i]] <- list(x = x, y = y)
+  }
+    # Insert each image into the PDF
+  for (i in seq_along(image_files)) {
+    if (file.exists(image_files[i])) {
+      image <- readPNG(image_files[i])
+      position <- positions[[i]]
+      grid.raster(image, x = position$x, y = position$y, width = width, height = height)
+    }
+  }
+
+  return(positions[[num_images]]$y - height/2 - y_spacing)
+}
+
+insert_deck_loading <- function(data, x_margin, y_initial, font_size, y_spacing) {
+  deck <- c("Deck Loading Instructions",
+                paste("Check that", data$pipette_name, "is in the", data$pipette_mount, "mount"),
+                paste("Slot", paste(data$pipette_tiprack_slot, collapse = ", "), ": load", data$pipette_tiprack_name, "for the", data$pipette_name, "pipette."),
+                paste("Slot", data$source_plate_slot, ": load", data$source_plate_name, "with source reagents."),
+                paste("Slot", data$destination_plate_slot, ": load", data$destination_plate_name, "as a destination plate."))
+  deck_y_lines <- y_initial - seq(0, length(deck) - 1) * y_spacing
+  text_style <- gpar(fontsize = font_size, fontface = c("bold", rep("plain", length(deck) - 1)))
+  grid.text(deck, x = x_margin, y = deck_y_lines, just = "left", gp = text_style)
+}
+
+instructions <- function(json_file_path, visualised_labware, output_file, x_margin = 0.05, y_spacing = 0.02, labware_width = 0.45, labware_height = 0.27, font_size = 12, y_initial = 0.98) {
+  pdf(output_file, width = 8.5, height = 11)
+  par(mar = c(5, 4, 4, 2) + 0.1)
+  json_data <- fromJSON(file = json_file_path)
+
+  overview <- insert_overview(json_data, x_margin, y_initial, y_spacing, font_size) # Title and Overview
+  preparation <- insert_preparation(x_margin, overview, y_spacing)   # Reagents preparation
+
+
+  labware <- insert_labware(visualised_labware, labware_width, labware_height, x_margin, preparation, y_spacing)   # # Insert images and get coordinates
+  deck_loading <- insert_deck_loading(json_data, x_margin, labware, font_size, y_spacing)
+
+  dev.off()
+
+}
+
+# Command-line arguments
+args <- commandArgs(trailingOnly = TRUE)
+json_file_path <- args[1]
+visualised_labware <- args[2]
+output_file <- args[3]
+
+# Generateinstructions
+instructions(json_file_path, visualised_labware, output_file)