Nothing
## ----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)
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