exaustive_gating_demo.R

devtools::load_all(".")
library(ggcyto)

load existing gating set

dataDir <- system.file("extdata",package="flowWorkspaceData")
gs <- load_gs(list.files(dataDir, pattern = "gs_manual",full = TRUE))

start from singlets node

gs2 <- clone(gs, isNew = FALSE, isEmpty = FALSE)
Rm("CD3+", gs2)
plot(gs2)

start the exaustive gating

gating("singlets", gs2, min.count = 2000 ,min.percent = 0.2, debug.mode = T, max.depth = -1)

## parent: singlets

## Loading required package: gridExtra

## selected marker: CD8

## parent: singlets/CD8+

## selected marker: CCR7

## parent: singlets/CD8+/CCR7+

## selected marker: CD45RA

## parent: singlets/CD8+/CCR7+/CD45RA+

## parent: singlets/CD8+/CCR7+/CD45RA-

## Warning: Removed 1 rows containing missing values (geom_point).

## selected marker: CD4

## skip node 'singlets/CD8+/CCR7+/CD45RA-/CD4+' due to the low cell count : 512

## skip node 'singlets/CD8+/CCR7+/CD45RA-/CD4-' due to the low cell count : 1899

## parent: singlets/CD8+/CCR7-

## selected marker: CD45RA

## parent: singlets/CD8+/CCR7-/CD45RA+

## selected marker: CD3

## parent: singlets/CD8+/CCR7-/CD45RA+/CD3+

## parent: singlets/CD8+/CCR7-/CD45RA+/CD3-

## parent: singlets/CD8+/CCR7-/CD45RA-

## parent: singlets/CD8-

## Warning: Removed 1 rows containing missing values (geom_point).

## selected marker: CD45RA

## parent: singlets/CD8-/CD45RA+

## Warning: Removed 1 rows containing missing values (geom_point).

## selected marker: CD4

## parent: singlets/CD8-/CD45RA+/CD4+

## parent: singlets/CD8-/CD45RA+/CD4-

## Warning: Removed 1 rows containing missing values (geom_point).

## Warning: Removed 1 rows containing missing values (geom_point).

## selected marker: HLA-DR

## parent: singlets/CD8-/CD45RA+/CD4-/HLA-DR+

## parent: singlets/CD8-/CD45RA+/CD4-/HLA-DR-

## parent: singlets/CD8-/CD45RA-

## Warning: Removed 1 rows containing missing values (geom_point).

## selected marker: CD38

## parent: singlets/CD8-/CD45RA-/CD38+

## Warning: Removed 1 rows containing missing values (geom_point).

## selected marker: CD3

## parent: singlets/CD8-/CD45RA-/CD38+/CD3+

## parent: singlets/CD8-/CD45RA-/CD38+/CD3-

## parent: singlets/CD8-/CD45RA-/CD38-

plot(gs2)

autoplot(gs2[[1]])

setDT(pData(gs))