## ----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)