In McConkeyLab/bladdr: A Helping Hand in McConkey Land

Analysis Parameters

Date: r Sys.Date()
Number of Primers: r params$n_primers
Primer Names: r params$primer_names
Plate Format: r params$format
Exclude Border? r params$exclude_border

Sample Preparation

sp <- params$sample_prep

colnames(sp) <- c("Sample", "[RNA]", names(sp)[-c(1:2)])

sp |> 
  gt::gt() |> 
  gt::fmt_number(c("diluted_rna_to_add", "water_to_add")) |> 
  gt::cols_label(
    dilution_factor = "Dil. Factor",
    diluted_concentration = "Dil. [RNA] ",
    diluted_rna_to_add = "Vol. dil. [RNA]",
    water_to_add = "Vol. H2O",
    final_vol = "Vol. final (uL)"
  ) |> 
  gt::tab_style(
    style = list(
      gt::cell_fill(color = "#2C5295"),
      gt::cell_text(color = "#FFFFFF"),
      gt::cell_borders(color = "#1C345F")
    ),
    locations = gt::cells_body()
  ) |>  
  gt::tab_style(
    style = list(
      gt::cell_fill(color = "#1C345F"),
      gt::cell_text(weight = "bold", color = "#FFFFFF"),
      gt::cell_borders(color = "#1C345F")
    ),
    locations = gt::cells_column_labels()
  ) |> 
  gt::tab_options(table.align = "left") |> 
  gt::tab_options(
    column_labels.border.bottom.color = "#1C345F"
  ) |> 
  gt::opt_table_outline(color = "#1C345F")

Mastermix Preparation

params$mm_prep |> 
  gt::gt() |>  
  gt::fmt_number(
    c("vol")
  ) |> 
  gt::cols_label(
    reagent = "Reagent",
    vol = "Volume (uL)"
  ) |> 
  gt::tab_style(
    style = list(
      gt::cell_fill(color = "#2C5295"),
      gt::cell_text(color = "#FFFFFF"),
      gt::cell_borders(color = "#1C345F")
    ),
    locations = gt::cells_body()
  ) |>  
  gt::tab_style(
    style = list(
      gt::cell_fill(color = "#1C345F"),
      gt::cell_text(weight = "bold", color = "#FFFFFF"),
      gt::cell_borders(color = "#1C345F")
    ),
    locations = gt::cells_column_labels()
  ) |> 
  gt::tab_options(table.align = "left") |> 
  gt::tab_options(
    column_labels.border.bottom.color = "#1C345F"
  ) |> 
  gt::opt_table_outline(color = "#1C345F")

Mastermix Layout

if(params$format == 96) {
  size <- 24
  size_text <- 8
} else {
  size <- 12
  size_text <- 4
}

ggplot2::ggplot(params$plate, ggplot2::aes(x = col, y = row, color = primer, label = primer_name)) + 
  ggplot2::geom_point(size = size) + 
  ggplot2::geom_text(color = "black", size = size_text, na.rm = TRUE) + 
  ggplot2::theme(legend.position = "none", plot.background = ggplot2::element_blank())

Sample Layout

plot_labels <- dplyr::arrange(params$plate, primer) |> 
  dplyr::pull(sample_name) |> 
  unique()

plot_labels <- plot_labels[which(!is.na(plot_labels))]
plot_labels <- c(plot_labels, NA)

ggplot2::ggplot(params$plate, ggplot2::aes(x = col, y = row, color = sample, label = plotting_name)) + 
  ggplot2::geom_point(size = size) + 
  ggplot2::geom_text(color = "black", size = size_text, na.rm = TRUE) +
  ggplot2::scale_color_hue(labels = plot_labels) + 
  ggplot2::theme(legend.position = "bottom", plot.background = ggplot2::element_blank())