QC for DC panel

library(flowCore)
library(flowWorkspace)
library(cytoqc)
# devtools::load_all()
path <- "~/remote/fh/fast/gottardo_r/mike_working/lyoplate_out/parsed"
centers <- c('BIIR','CIMR','Miami','NHLBI','Stanford','UCLA','Yale')

Load gs

panel <- "DC"
gslist <- sapply(centers, function(center) {
  message("Center: ", center)
  gs <- load_gs(file.path(path, center, panel), select = 1)
})

Check marker

cqc_data <- cqc_gs_list(gslist)
check_res <- cqc_check(cqc_data, "marker")
check_res
group_id nGatingSet marker
1 1 CD11c PE-Cy7, CD123 PerCP-Cy55, CD14 V450, CD16 APC, CD56 PE, HLA-DR V500, Lineage APC-H7, Live Dead FITC
2 1 CD11c, CD123, CD14, CD16, CD3_CD19_CD20, CD56, HLADR, LIVE_GREEN
3 1 CD11C, CD123, CD14, CD16, CD3+19+20, CD56, HLA-DR, LIVE DEAD
4 1 CD11c, CD123, CD14, CD16, CD3+CD19+CD20+, CD56, HLA-DR, Live Green
5 1 CD11c, CD123, CD14, CD16, CD3+CD19+CD20, CD56, HLA DR, Live/Dead
6 1 CD11c, CD123, CD14, CD16, CD3+CD19+CD20, CD56, HLA-DR, Live Green
7 1 CD11c, CD123, CD14, CD16, CD3CD19CD20, CD56, HLA-DR, LIVE

Match reference

match_res <- cqc_match(check_res, ref = 7)
match_res

Apply the match

cqc_fix(match_res)
cqc_check(cqc_data, "marker")
group_id nGatingSet marker
1 7 CD11c, CD123, CD14, CD16, CD56, HLA-DR, LIVE

Check panel

res <- cqc_check(cqc_data, "panel", by = "marker")
res
marker group 1(n=1) group 2(n=1) group 3(n=1) group 4(n=1) group 5(n=2) group 6(n=1)
CD11c <PE-Cy7 YG-A> <PE-Cy7-A> <PE Cy7 YG-A> <PE-Cy7-A> <PE-Cy7-A> <G780-A>
CD123 <PerCP-Cy5-5-A> <PerCP-Cy5-5-A> <PerCP-Cy5-5-A> <PerCP-Cy5-5-A> <PerCP-Cy5-5-A> <B710-A>
CD14 <Pacific Blue-A> <Pacific Blue-A> <Pacific Blue-A> <BD Horizon V450-A> <V450-A> <V450-A>
CD16 <APC-A> <APC-A> <APC-A> <APC-A> <APC-A> <R660-A>
CD56 <PE YG-A> <PE-A> <PE-A> <PE-A> <PE-A> <G560-A>
HLA-DR <AmCyan-A> <Am Cyan-A> <AmCyan-A> <BD Horizon V500-A> <V500-A> <V545-A>
LIVE <Alexa Fluor 488-A> <FITC-A> <FITC-A> <FITC-A> <FITC-A> <B515-A>

Standarize the panel

res <- cqc_match(res, ref = 2)
res
marker group 1(n=1) Ref group group 3(n=1) group 4(n=1) group 5(n=2) group 6(n=1)
CD11c <PE-Cy7 YG-A> <PE-Cy7-A> <PE Cy7 YG-A> <PE-Cy7-A> <PE-Cy7-A> <G780-A>
CD123 <PerCP-Cy5-5-A> <PerCP-Cy5-5-A> <PerCP-Cy5-5-A> <PerCP-Cy5-5-A> <PerCP-Cy5-5-A> <B710-A>
CD14 <Pacific Blue-A> <Pacific Blue-A> <Pacific Blue-A> <BD Horizon V450-A> <V450-A> <V450-A>
CD16 <APC-A> <APC-A> <APC-A> <APC-A> <APC-A> <R660-A>
CD56 <PE YG-A> <PE-A> <PE-A> <PE-A> <PE-A> <G560-A>
HLA-DR <AmCyan-A> <Am Cyan-A> <AmCyan-A> <BD Horizon V500-A> <V500-A> <V545-A>
LIVE <Alexa Fluor 488-A> <FITC-A> <FITC-A> <FITC-A> <FITC-A> <B515-A> 
cqc_fix(res)
cqc_check(cqc_data, "panel")
channel group 1(n=7)
<Am Cyan-A> HLA-DR
<APC-A> CD16
<FITC-A> LIVE
<Pacific Blue-A> CD14
<PE-A> CD56
<PE-Cy7-A> CD11c
<PerCP-Cy5-5-A> CD123

check gates

res <- cqc_check(cqc_data, "gate")
res
group_id nGatingSet gate
3 5 11c- 123-, 11c- 123+, 11c+ 123-, 11c+ 123+, 14+ 16+, 16- 56-, 16- 56+, 16+ 56-, 16+ 56+, DR+, Lin- 14-, Lin- 14+, MNC, not dead, root, singlets
1 1 11c - 123+, 11c- 123-, 11c+ 123-, 11c+ 123+, 14+ 16+, 16- 56-, 16- 56+, 16+ 56-, 16+ 56+, DR+, Lin- 14-, Lin- 14+, MNC, not dead, root, singlets
2 1 11c- 123-, 11c- 123+, 11c+ 123-, 11c+ 123+, 14+ 16+, 16- 56-, 16- 56+, 16+ 56-, 16+ 56+, DR+, Lin- 14-, Lin- 14+, MNC, not dead, root 
diff(res)
group_id nGatingSet gate
3 5 11c- 123+, singlets
1 1 11c - 123+, singlets
2 1 11c- 123+ 
match_res <- cqc_match(res, ref = 2)
match_res

Singlets are not important for analysis thus can be safely deleted (actually hidden)

cqc_fix(match_res)

Check channel again

res <- cqc_check(cqc_data, "channel")
res
group_id nGatingSet channel
1 2 <Am Cyan-A>, <APC-A>, <APC-Cy7-A>, <FITC-A>, <Pacific Blue-A>, <PE-A>, <PE-Cy7-A>, <PerCP-Cy5-5-A>, FSC-A, FSC-H, FSC-W, SSC-A, SSC-H, SSC-W, Time
2 1 <Am Cyan-A>, <APC-A>, <APC-Cy7-A>, <FITC-A>, <Pacific Blue-A>, <PE-A>, <PE-Cy7-A>, <PerCP-Cy5-5-A>, FSC-A, FSC-W, SSC-A, SSC-W, Time
3 1 <Am Cyan-A>, <APC-A>, <APC-Cy7-A>, <FITC-A>, <Pacific Blue-A>, <PE-A>, <PE-Cy7-A>, <PerCP-Cy5-5-A>, FSC-A, SSC-A, Time
4 1 <Am Cyan-A>, <APC-A>, <APC-H7-A>, <FITC-A>, <Pacific Blue-A>, <PE-A>, <PE-Cy7-A>, <PerCP-Cy5-5-A>, FSC-A, FSC-H, FSC-W, SSC-A, SSC-H, SSC-W, Time
5 1 <Am Cyan-A>, <APC-A>, <APC-H7-A>, <FITC-A>, <Pacific Blue-A>, <PE-A>, <PE-Cy7-A>, <PerCP-Cy5-5-A>, FSC-A, FSC-H, SSC-A, SSC-H, Time
6 1 <Am Cyan-A>, <APC-A>, <FITC-A>, <Pacific Blue-A>, <PE-A>, <PE-Cy7-A>, <PerCP-Cy5-5-A>, <R780-A>, FSC-A, FSC-H, FSC-W, SSC-A, SSC-H, SSC-W, Time 
match_res <- cqc_match(res, ref = 4)
match_res

W/H scatter are for singlets gate thus can be safely removed

cqc_fix(match_res)

Merge the standarized data

gs <- merge_list_to_gs(gslist)
gs
## A GatingSet with 7 samples