In calabrialab/ISAnalytics: Analyze gene therapy vector insertion sites data identified from genomics next generation sequencing reads for clonal tracking studies

knitr::opts_chunk$set(echo = FALSE, warning = FALSE)
options(DT.warn.size = FALSE)
library(flexdashboard)
library(DT)
found_color <- "#77d983"
not_found_color <- "#e36868"
secondary_col <-  "#ff9470"
proj_col <- params$set_vars$proj_col
pool_col <- params$set_vars$pool_col
launch_params <- if (is.null(params$launch_params) ||
                     purrr::is_empty(params$launch_params)) {
  NULL
} else {
    params$launch_params
  }

Files report {data-orientation=rows}

Row1

n_proj <- length(unique(params$files_found[[proj_col]]))
n_pools <- length(unique(params$files_found[[pool_col]]))
n_anomalies <- length(params$files_found$Anomalies[
  params$files_found$Anomalies])

Projects

valueBox(value = n_proj, icon = "glyphicon-inbox")

Pools

valueBox(value = n_pools, icon = "fa-folder")

Anomalies detected

valueBox(value = n_anomalies, icon = "glyphicon-warning-sign", color = secondary_col)

Row2 {data-height=100}

Set arguments

content <- paste0(
  c("<ul>", 
    paste0("<li><b>Chosen file patterns</b>: ", 
          paste0("'", launch_params$patterns, "'", collapse = ", "), 
          "</li>"), 
  paste0("<li><b>Matching option</b>: '", launch_params$matching_opt, "'</li>"),
  "</ul>"))
cat(content)

content <- paste("No patterns were set for this automated import operation")
cat(content)

Row3 {data-height=600 .tabset .tabset-fade}

collapse_file_names <- function(names) {
  if (all(is.na(names))) {
    return(NA_character_)
  }
  return(
    paste0(paste0(paste0("<b>", seq_len(length(names)), ")</b> "), 
                  names), collapse = "<br/>")
  )
}
formatted_files <- params$files_found$Files |>
  purrr::map(~ {
    .x |>
      dplyr::group_by(.data$Quantification_type) |>
      dplyr::summarise(Files_found = collapse_file_names(.data$Files_found), 
                       .groups = "drop")
  })
files_details <- purrr::map2(formatted_files, params$files_found$Files_count,
                             ~ {
                               .x |>
                                 dplyr::inner_join(.y, 
                                                   by = "Quantification_type")
                             })

count_details <- params$files_found |>
  dplyr::mutate(files_details = files_details) |>
  dplyr::select(-.data$Files, -.data$Anomalies, -.data$Files_count)  |>
  tidyr::unnest(.data$files_details) |>
  dplyr::mutate(
    !!proj_col := as.factor(.data[[proj_col]]),
    !!pool_col := as.factor(.data[[pool_col]]),
    Quantification_type = as.factor(.data$Quantification_type))

Files details by quantification

found_render <- JS("function(data, type, row) {",
                   "var icn = ",'"\u2713"', ";",
                   "var clss = ", '"text-success"', ";",
                   "if (data == 0) {",
                   "icn = ",'"\u2715"',";",
                   "clss = ", '"text-danger"', ";",
                   "} else if (data > 1) {",
                   "icn = ",'"\u26A0"', ";",
                   "clss = ", '"text-warning"', ";",
                   "}",
                   "return '<span class='+clss+'>'+data.toString()+' '+icn+",
                   "'</span>'",
                   "}")
datatable(
  count_details, rownames = FALSE, 
  colnames = stringr::str_replace_all(colnames(count_details), "_", " "), 
  filter = 'top',
  escape = FALSE,
  options = list(
    columnDefs = list(
      list(targets = 4,
           render = found_render)
      ),
      scrollY = 350
    ),
) |> formatStyle(columns = 5, fontWeight = 'bold', textAlign = 'center')

About

Summary of files found for each project/pool and quantification requested.
If duplicated files are found you will find a 'warning' symbol next to the corresponding number. Please remember that in automatic mode the function tries to discriminate between duplicates according to the provided patterns, if no choice can be made, all files are discarded.

If no files were found for the corresponding quantification you will see a 'cross' symbol.

Import summary {data-orientation=rows}

Row1

not_imported <- length(params$files_imp$Imported[
  params$files_imp$Imported == FALSE])
tot_samples <- sum(params$files_imp$Number_of_samples, na.rm = TRUE)

Files not imported

gauge(not_imported, min = 0, max = nrow(params$files_imp), 
      sectors = gaugeSectors(danger = c(1, nrow(params$files_imp))))

Total samples

valueBox(value = tot_samples)

Row2 {data-height=600 .tabset .tabset-fade}

Summary of files imported

files_imp <- params$files_imp |>
  dplyr::mutate(dplyr::across(c(.data[[proj_col]], 
                              .data[[pool_col]], 
                              .data$Quantification_type), .fns = as.factor))
datatable(
  files_imp,
  class = "stripe",
  filter = "top", 
  rownames = FALSE,
  colnames = stringr::str_replace_all(colnames(files_imp), "_", " "),
  options = list(
            order = list(list(4, 'asc')),
            scrollY = 350
          )
) |> formatStyle(columns = "Imported", 
              color = styleEqual(
                levels = c(TRUE, FALSE),
                values = c(found_color, not_found_color)
              ), fontWeight = "bold", textTransform = "uppercase")

cat("*Nothing to report*")

About

Summary of files chosen for import. If Imported is false, something may have gone wrong during the import phase (most likely I/O errors).

Annotation issues {data-orientation=rows}

Row1 {data-height=600 .tabset .tabset-fade}

Possible annotation problems

datatable(
  params$annot_prob,
  rownames = FALSE, 
  colnames = stringr::str_replace_all(colnames(files_details), "_", " "), 
  filter = 'top', options = list(scrollY = 350)
)

cat("*Nothing to report*")

About

Report on annotation issues. Here are reported, if found, integration sites that have been annotated with 2 or more different genes. If the table isn't empty, you might want to check your matrices or re-perform the annotation step.

Reproducibility {data-orientation=rows}

Row1 {data-height=600}

Session info {style="width: 95% !important"}

sessionInfo()

calabrialab/ISAnalytics documentation built on Nov. 2, 2023, 8:57 p.m.