LIST_ComputeDatatableOptions: LIST_ComputeDatatableOptions Insert data table options for...

In 47Lies/isoformnspectRe: Companion package of a nextflow pipeline

Description

LIST_ComputeDatatableOptions Insert data table options for automatic inclusion of sparkline javascript code. Need some very secific DATA

Usage

LIST_ComputeDatatableOptions(
  LIST_SampleNames,
  TYPE = "Skeleton",
  LIST_SparlinesOptions = list(type = "bar", height = 40, width = 60, highlightColor =
    "red", chartRangeMin = 0, chartRangeMax = 1, tooltipFormat =
    "{{offset:offset}} {{value.2}}")
)

Arguments

LIST_SampleNames	List of sample names that will be included for the sparkline
TYPE	if it has to be included in a skeleton part or if it has to be included in the app
LIST_SparlinesOptions	options to be included in the sparkline

Value

List of options that will be included in a DT::data.table

Examples

library(data.table)
library(DT)
library(sparkline)
library(htmlwidgets)
P_FilePath <- system.file("extdata",
 "peptides.example.txt",
  package = "isoformnspectRe")
Peptides<-fread(
 P_FilePath,
 integer64="double")
SampleNames<-list("siNT"=c("siNT_48-1",
"siNT_48-2",
"siNT_48-3",
"siNT_72-1",
"siNT_72-2",
"siNT_72-3"),
"siSF3B1"=c("siSF3B1-1",
"siSF3B1-2",
"siSF3B1-3",
"siSRSF1-1",
"siSRSF1-2",
"siSRSF1-3"))
Samples <- unlist(SampleNames)
MaxIntensities <- apply(Peptides[,paste("Intensity",Samples),with=FALSE],1,max)
Peptides[,
 (paste("Intensity",Samples)) := lapply(.SD, function(x) x/MaxIntensities),
  .SDcols = paste("Intensity",Samples)]
Peptides[,"siNT Infos" := paste(.SD, collapse = ","), .SDcols =
paste("Intensity",SampleNames[["siNT"]]), by = Sequence]
Peptides[,"siSF3B1 Infos" := paste(.SD, collapse = ","), .SDcols =
paste("Intensity",SampleNames[["siSF3B1"]]), by = Sequence]
PeptideColumnOfInterest<-c("Proteins","Sequence",
"siNT Infos","siSF3B1 Infos",
"Start position","End position","PEP")
LocalDatatable <- DT::datatable(
Peptides[,..PeptideColumnOfInterest],
width = "100%",
options = LIST_ComputeDatatableOptions(LIST_SampleNames=SampleNames),
rownames = FALSE, escape = FALSE)
LocalDatatable$dependencies <- append(LocalDatatable$dependencies,
 htmlwidgets:::getDependency("sparkline"))
LocalDatatable

47Lies/isoformnspectRe documentation built on May 29, 2021, 3 p.m.