In davidsbutcher/CRawFISh: Create summary info from a tdReport or directory of Thermo Raw files.

library(magrittr)
library(purrr)
library(glue)
library(dplyr)
library(flexdashboard)
library(DT)
library(htmlwidgets)
library(ggplot2)

knitr::opts_chunk$set(echo = FALSE)

r paste('#', "SUMMARY", '{data-navmenu="Raw Filename"}')

Column {.tabset .tabset-fade data-height=800}

Raw File List

This is an automatically generated document containing CRawFISh analysis results for the following .raw files:

rawFileList %>%
  map(basename) %>%
  set_names(NULL) %>% 
  pander::pander()

Metadata Summary

NOTE: Multiple columns are hidden by default, click "Column Visibility" to view them.

rawFileInfoSum %>% 
  dplyr::mutate_at(c(14,15,17,18,19,21,22,24), ~format(., scientific = 4, digits = 4, nsmall = 3)) %>%
  dplyr::rename(
    "Filename" = filename,
    "Scan Segment" = ScanSegment,
    "Scan Event" = ScanEvent,
    "Polarity" = polarity,
    "MS Order" = MSOrder,
    "Analyzer" = MassAnalyzer,
    "Scan Header" = scanHeader,
    "FT Resolution" = FTResolution
  ) %>% 
  DT::datatable(
    extensions = c("FixedColumns", "Buttons", "Scroller"),
    class = "hover",
    options = list(
      deferRender = TRUE,
      scrollY = 600,
      scrollX = TRUE,
      scroller = TRUE,
      columnDefs = list(
        list(
          visible = FALSE,
          targets = c(9:length(rawFileInfoSum))
        ),
        list(
          className = 'dt-center'
        )
      ),
      dom = "Bfrtip",
      fixedColumns = list(leftColumns = 2),
      buttons = c("copy", "csv", "excel", "colvis")
    )
  ) %>% 
  formatStyle(1:length(rawFileInfoSum), fontSize = "9")

out <- NULL

options(knitr.duplicate.label = 'allow')

for (i in seq_along(rawFileList)) {

  out <- c(out, knitr::knit_child("generate_report_child.Rmd"))

}

r paste(knitr::knit_child(text = out), collapse = '')

davidsbutcher/CRawFISh documentation built on July 7, 2021, 1:03 p.m.