inst/doc/HowToWriteCSVTemplate.R

In openCyto: Hierarchical Gating Pipeline for flow cytometry data

## ----setup, include=FALSE-----------------------------------------------------
library(knitr)
opts_chunk$set(out.extra='style="display:block; margin: auto"', fig.align="center", message = FALSE, warning = FALSE, knitr.table.format = "markdown")
assign("depthtrigger", 60, data.table:::.global)

## ----init, echo=F-------------------------------------------------------------
library(openCyto)
library(data.table)

template_row <- data.table(alias = "TH", pop = "+-"
                          , parent = "cd3", dims = "cd4,cd8"
                          , gating_method = "mindensity", gating_args = ""
                          , collapseDataForGating = "TRUE", groupBy = "4"
                          , preprocessing_method = "", preprocessing_args = ""
                      )



## ----A+/-(before), echo = F, results = "asis"---------------------------------
	this_row <- copy(template_row)	
	this_row[, pop := "+/-"]
	this_row[, alias := "*"]
	this_row[, dims := "cd4"]
	kable(this_row[, 1:6, with = F])

## ----A+/-(after), echo = F, results = "asis"----------------------------------
      kable(openCyto:::.preprocess_row(this_row)[, 1:6, with = F])
      

## ----A+B+(before), echo = F, results = "asis"---------------------------------
	this_row <- copy(template_row)	
	this_row[, pop := "+-"]
	this_row[, alias := "T helper"]
	kable(this_row[, 1:6, with = F])

## ----A+B+(after), echo = F, results = "asis"----------------------------------
      kable(openCyto:::.preprocess_row(this_row)[, 1:6, with = F])

## ----A+/-B+/-(before), echo = F, results = "asis"-----------------------------
	this_row <- copy(template_row)	
	this_row[, pop := "+/-+/-"]
	this_row[, alias := "*"]
	kable(this_row[, 1:6, with = F])

## ----A+/-B+/-(after), echo = F, results = "asis"------------------------------
      kable(openCyto:::.preprocess_row(this_row)[, 1:6, with = F])

## ----multiPop(before), echo = F, results = "asis"-----------------------------
	this_row <- copy(template_row)	
	this_row[, pop := "*"]
	this_row[, alias := "CD4,CD8"]
	this_row[, gating_method := "curv2gate"]
	kable(this_row[, 1:6, with = F])

## ----multiPop(after), echo = F, results = "asis"------------------------------
      kable(openCyto:::.preprocess_row(this_row)[, 1:6, with = F])

## ----multiPop_noExpand(before), echo = F, results = "asis"--------------------
	this_row[, alias := "*"]
	kable(this_row[, 1:6, with = F])

## ----multiple_parents, echo=F, results='asis'---------------------------------
	this_row[, alias := "IL2+"]
  this_row[, pop := "+"]
  this_row[, parent := "cd4,cd8"]
  this_row[, dims := "IL2"]
  this_row[, gating_method := "refGate"]
  this_row[, gating_args := "cd3/IL2+"]
	kable(this_row[, 1:6, with = F])

## ----multiple_parents_expand, echo=F, results='asis'--------------------------
kable(openCyto:::.split_multi_parents(this_row)[, 1:6, with = F])

## ----finalizer, include=FALSE-------------------------------------------------
assign("depthtrigger", 3, data.table:::.global)