QC for SDY 820

library(flowCore)
library(flowWorkspace)
# library(cytoqc)
devtools::load_all()

path <- "~/remote/fh/fast/gottardo_r/mike_working/SDY820"

parse ws

library(CytoML)
ws <- open_flowjo_xml(file.path(path, "All TB mem samples centralised New gating-1.605759.wsp"))
gs1 <- flowjo_to_gatingset(ws, name = 2)
gs2 <- flowjo_to_gatingset(ws, name = 3)
save_gs(gs1, file.path(path, "parsed", "gs1"))
save_gs(gs2, file.path(path, "parsed", "gs2"))

Load gs

gslist <- list(load_gs(file.path(path, "parsed", "gs1"), select = 1:2)
                ,load_gs(file.path(path, "parsed", "gs2"), select = 1:2)
                )
cqc_data <- cqc_gs_list(gslist)

Check marker

check_res <- cqc_check(cqc_data, "marker")
check_res

group_id	nGatingSet	marker
1	2	CCR7, CD14, CD19, CD25, CD3, CD4, CD45RA, CD56, CD8, LD

Check channel

check_res <- cqc_check(cqc_data, "channel")
check_res

group_id	nGatingSet	channel
1	1	Comp-Alexa Fluor 700-A, Comp-APC-A, Comp-APC-eFluor 780-A, Comp-BV650-A, Comp-eFluor 450-A, Comp-FITC-A, Comp-PE-A, Comp-PE-Cy7-A, Comp-PerCP-Cy5-5-A, Comp-V500-A, FSC-A, FSC-H, FSC-W, SSC-A, SSC-H, SSC-W, Time
2	1	Comp-Alexa Fluor 700-A, Comp-APC-A, Comp-APC-eFluor780-A, Comp-BV650-A, Comp-eFluor450-A, Comp-FITC-A, Comp-PE-A, Comp-PE-Cy7-A, Comp-PerCP-Cy5-5-A, Comp-V500-A, FSC-A, FSC-H, FSC-W, SSC-A, SSC-H, SSC-W, Time

Match reference

match_res <- cqc_match(check_res, ref = 1)
match_res

Apply the match

cqc_fix(match_res)
cqc_check(cqc_data, "marker")

group_id	nGatingSet	marker
1	2	CCR7, CD14, CD19, CD25, CD3, CD4, CD45RA, CD56, CD8, LD

Check panel

res <- cqc_check(cqc_data, "panel")
format(res, anchor = "marker")

check gates

res <- cqc_check(cqc_data, "gate")
res

group_id	nGatingSet	gate
1	2	CD14-, CD14+ Monocytes, CD3-CD19+ B cells, CD3-CD56+ NK, CD3+CD56- conv T cells, CD3+CD56+ NKT, CD3hiCD56+ NKT, CD4 T cells, CD4 T cells/Q1: CD45RA- , CCR7+, CD4 T cells/Q2: CD45RA+ , CCR7+, CD4 T cells/Q3: CD45RA+ , CCR7-, CD4 T cells/Q4: CD45RA- , CCR7-, CD4+CD25+ Tregs, CD8 T cells, CD8 T cells/Q1: CD45RA- , CCR7+, CD8 T cells/Q2: CD45RA+ , CCR7+, CD8 T cells/Q3: CD45RA+ , CCR7-, CD8 T cells/Q4: CD45RA- , CCR7-, Cells, Live, root, Single Cells FSC, Single Cells SSC

Merge the standarized data

gs <- merge_list_to_gs(gslist)
gs

## A GatingSet with 4 samples