A QC tool for openCyto

The basic workflow:

Run cqc_group to see the summary
cqc_match_reference and cqc_find_solution for selected groups
cqc_fix based on the solution or cqc_drop_groups for unsolvable issues
Iterate 1~3 steps until data is cleaned
split the data into multiple sets for multi-panel cases

library(flowCore)
library(flowWorkspace)
# library(cytoqc)
devtools::load_all("../")

Load the FCS

files <- list.files(data_dir, ".fcs", full.names = TRUE)
cqc_data <- cqc_load_fcs(files)
cqc_data

## cytoqc data: 
## 35  samples

QC check for channel

groups <- cqc_group(cqc_data, "channel")
su <- summary(groups)
su

group_id	nFCS	channel
3	32	FL1-H, FL2-A, FL2-H, FL3-H, FL4-H, FSC-H, SSC-H, Time
1	1	channelA, FL1-H, FL2-A, FL2-H, FL3-H, FL4-H, FSC-H, SSC1-H, Time
2	1	FL1-H, FL2-A, FL2-H, FL3-H, FL4-H, fsc-h, SSC-H
4	1	FL1-H, FL2-A, FL2-H, FL3-H, FL4-H, fsc-h, SSC1-H, Time

diff(su)

group_id	nFCS	channel
3	32	FSC-H, SSC-H, Time
1	1	channelA, FSC-H, SSC1-H, Time
2	1	fsc-h, SSC-H
4	1	fsc-h, SSC1-H, Time

Match against the reference to find discrepancy

match_result <-  cqc_match_reference(groups, ref = 3, select = c(1, 4))
match_result

group_id	Not in reference	Missing channels
1	channelA,SSC1-H	SSC-H
4	fsc-h,SSC1-H	FSC-H,SSC-H

Recommend the solution

solution <- cqc_find_solution(match_result)
solution

Proposed change
SSC1-H –> SSC-H
channelA
fsc-h –> FSC-H

Show the itemized details

knit_print(solution, itemize = TRUE)

group_id	Proposed change
1	SSC1-H –> SSC-H
1	channelA
4	fsc-h –> FSC-H
4	SSC1-H –> SSC-H

Export/import the `solution` for revision (if needed)

library(readr)
write_csv(solution, csvfile)
#manually edit csvfile and load it back
solution_revised <- read_csv(csvfile)

Apply the fix

cqc_fix(solution)

Refresh QC report

groups <- cqc_group(cqc_data, "channel")
summary(groups)

group_id	nFCS	channel
2	34	FL1-H, FL2-A, FL2-H, FL3-H, FL4-H, FSC-H, SSC-H, Time
1	1	FL1-H, FL2-A, FL2-H, FL3-H, FL4-H, fsc-h, SSC-H

Drop groups that can not be fixed

groups <- cqc_drop_groups(groups, 1)
cqc_data <- cqc_get_data(groups)
length(cqc_data)

## [1] 34

QC for marker

#summarise marker groups
groups <- cqc_group(cqc_data, "marker")
su <- summary(groups)
diff(su)

group_id	nFCS	marker
3	21	CD15 FITC, CD33 APC, Time (102.40 sec.)
5	7	CD15 FITC, CD33 APC, Time (51.20 sec.)
4	4	CD15 FITC, CD33 APC, Time (204.80 sec.)
1	1	apc cd33, cd15, Time (102.40 sec.)
2	1	CD15 FITC, CD33 APC, markerA, Time (204.80 sec.)

Pick references and groups to fix

solution <- cqc_find_solution(groups, ref = 3, select = 1, max.distance = 0.4) 
solution

Proposed change
cd15 –> CD15 FITC
apc cd33 –> CD33 APC

cqc_fix(solution)

solution <- cqc_find_solution(groups, ref = 4, select = 2, max.distance = 0.4) 
solution

Proposed change
markerA

cqc_fix(solution)

update checks

groups <- cqc_group(cqc_data, "marker")
su <- summary(groups)
diff(su)

group_id	nFCS	marker
1	22	Time (102.40 sec.)
3	7	Time (51.20 sec.)
2	5	Time (204.80 sec.)

split by groups

data_list <- split(groups)
data_list

## $`1`
## cytoqc data: 
## 22  samples 
## 
## $`2`
## cytoqc data: 
## 5  samples 
## 
## $`3`
## cytoqc data: 
## 7  samples

QC for panel

# first data set is already clean
summary(cqc_group(data_list[[1]], "panel"))

channel	marker	group_id	nFCS
FL1-H	CD15 FITC	1	22
FL2-H	CD45 PE
FL3-H	CD14 PerCP
FL4-H	CD33 APC
FSC-H	FSC-Height
SSC-H	SSC-Height
Time	Time (102.40 sec.)

Save the cleaned data as FCS

cleaned <- data_list[[1]]

out <- tempfile()
write_fcs(cleaned, out)

Or Coerce it directly into `cytoset` (zero-copying)

cs <- cytoset(cleaned)
cs

## A cytoset with 22 samples.
## 
##   column names:
##     FSC-H, SSC-H, FL1-H, FL2-H, FL3-H, FL2-A, FL4-H, Time

Further split the data by panel

grps <- cqc_group(data_list[[2]], "panel")
diff(summary(grps))

channel	marker	group_id	nFCS
FL1-H	CD15 FITC	1	4
FL2-H	CD45 PE	1	4
FL1-H	CD45 PE	2	1
FL2-H	CD15 FITC	2	1

split(grps)

## $`1`
## cytoqc data: 
## 4  samples 
## 
## $`2`
## cytoqc data: 
## 1  samples

A QC tool for openCyto

cytoqc – A QC tool for openCyto

The basic workflow:

Load the FCS

QC check for channel

Match against the reference to find discrepancy

Recommend the solution

Export/import the solution for revision (if needed)

Apply the fix

Refresh QC report

Drop groups that can not be fixed

QC for marker

Pick references and groups to fix

update checks

split by groups

QC for panel

Save the cleaned data as FCS

Or Coerce it directly into cytoset (zero-copying)

Further split the data by panel

Export/import the `solution` for revision (if needed)

Or Coerce it directly into `cytoset` (zero-copying)