FCS file information

# HG changeset patch # User azomics # Date 1592951642 14400 # Node ID 34397a84faf1e79c2b5490a34d84ad1e2b09ca81 # Parent 60aa5e56531a7d0d7ac6e4231003a6a4af5c0f70 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowai commit 83ef47729f2d2cdae84171761a6795df9fb63389" diff -r 60aa5e56531a -r 34397a84faf1 FCSflowAI.R --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/FCSflowAI.R Tue Jun 23 18:34:02 2020 -0400 @@ -0,0 +1,38 @@ +#!/usr/bin/env Rscript +# +# Authors: Gianni Monaco +# +# Reference: flowAI: automatic and interactive anomaly discerning +# tools for flow cytometry data. +# Gianni Monaco, Hao Chen, Michael Poidinger, Jinmiao Chen, +# Joao Pedro de Magalhaes and Anis Larbi +# Bioinformatics (2016) +# doi: 10.1093/bioinformatics/btw191 +# + +library(flowAI) +library(methods) + +# parse arguments + +args <- commandArgs(trailingOnly = TRUE) + +remFS <- if(args[4]) c("FSC", "SSC") else NULL + +flow_auto_qc( + fcsfiles = args[1], + remove_from = args[2], + alphaFR = as.numeric(args[3]), + ChRemoveFS = remFS, + outlierFS = args[5], + pen_valueFS = as.numeric(args[6]), + sideFM = args[7], + fcs_QC = ifelse(args[9] == "None", FALSE, "_QC"), + fcs_highQ = ifelse(args[10] == "None", FALSE, "_highQ"), + fcs_lowQ = ifelse(args[11] == "None", FALSE, "_lowQ"), + folder_results = FALSE) + +try(file.rename(dir(".", pattern = ".*_QC.html"), args[8]), silent =TRUE) +try(file.rename(dir(".", pattern = ".*_QC.fcs"), args[9]), silent =TRUE) +try(file.rename(dir(".", pattern = ".*_highQ.fcs"), args[10]), silent =TRUE) +try(file.rename(dir(".", pattern = ".*_lowQ.fcs"), args[11]), silent =TRUE) diff -r 60aa5e56531a -r 34397a84faf1 FCSflowAI.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/FCSflowAI.xml Tue Jun 23 18:34:02 2020 -0400 @@ -0,0 +1,177 @@ + + automatic quality control + + bioconductor-flowcore + bioconductor-flowai + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + (highQ_FCS) + + + (lowQ_FCS) + + + (QC_FCS) + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 10.1093/bioinformatics/btw191 + + diff -r 60aa5e56531a -r 34397a84faf1 flowai/FCSflowAI.R --- a/flowai/FCSflowAI.R Mon Feb 27 12:55:30 2017 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,41 +0,0 @@ -# -# -# Authors: Gianni Monaco -# -# Reference: flowAI: automatic and interactive anomaly discerning -# tools for flow cytometry data. -# Gianni Monaco, Hao Chen, Michael Poidinger, Jinmiao Chen, -# Joao Pedro de Magalhaes and Anis Larbi -# Bioinformatics (2016) -# doi: 10.1093/bioinformatics/btw191 -# - -library(flowAI) -library(methods) - -# parse arguments - -args <- commandArgs(trailingOnly = TRUE) - -remFS <- if(args[5]) c("FSC", "SSC") else NULL - -flow_auto_qc( - fcsfiles = args[2], - remove_from = args[3], - alphaFR = as.numeric(args[4]), - ChRemoveFS = remFS, - outlierFS = args[6], - pen_valueFS = as.numeric(args[7]), - sideFM = args[8], - fcs_QC = ifelse(args[10] == "None", FALSE, "_QC"), - fcs_highQ = ifelse(args[11] == "None", FALSE, "_highQ"), - fcs_lowQ = ifelse(args[12] == "None", FALSE, "_lowQ"), - folder_results = FALSE) - -try(file.rename(dir(".", pattern = ".*_QC.html"), args[9]), silent =TRUE) -try(file.rename(dir(".", pattern = ".*_QC.fcs"), args[10]), silent =TRUE) -try(file.rename(dir(".", pattern = ".*_highQ.fcs"), args[11]), silent =TRUE) -try(file.rename(dir(".", pattern = ".*_lowQ.fcs"), args[12]), silent =TRUE) - - - diff -r 60aa5e56531a -r 34397a84faf1 flowai/FCSflowAI.xml --- a/flowai/FCSflowAI.xml Mon Feb 27 12:55:30 2017 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,178 +0,0 @@ - - automatic quality control - - r - bioconductor-flowcore - bioconductor-flowai - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - (highQ_FCS) - - - (lowQ_FCS) - - - (QC_FCS) - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 10.1093/bioinformatics/btw191 - - diff -r 60aa5e56531a -r 34397a84faf1 flowai/static/images/flowtools/autoflowrate.png Binary file flowai/static/images/flowtools/autoflowrate.png has changed diff -r 60aa5e56531a -r 34397a84faf1 flowai/static/images/flowtools/autosignal.png Binary file flowai/static/images/flowtools/autosignal.png has changed diff -r 60aa5e56531a -r 34397a84faf1 flowai/static/images/flowtools/margins.png Binary file flowai/static/images/flowtools/margins.png has changed diff -r 60aa5e56531a -r 34397a84faf1 flowai/test-data/input.fcs Binary file flowai/test-data/input.fcs has changed diff -r 60aa5e56531a -r 34397a84faf1 flowai/test-data/nooutliers/QCreport_nooutliers.html --- a/flowai/test-data/nooutliers/QCreport_nooutliers.html Mon Feb 27 12:55:30 2017 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,240 +0,0 @@ - - - - - -FCS file information - - - - - - - - - - - - - - -

FCS file information

- -

-
Input file name: dataset_934
-Number of events: 20000
-

- -

Quality control analysis

- -

Summary

- -

-
The anomalies were removed from: Flow Rate, Flow Signal and Flow Margin
-Anomalies detected in total: 25.11 %
-Number of high quality events: 14978
-

- -

Flow rate check

- -

-
0 % anomalies detected in the flow rate check.
-

- -

It was not possible to analyze the flow rate since the time channel is missing.

- -

Signals acquisition check

- -

-
0 % anomalies detected in the signal aquisition check.
-

- -

Outliers were removed before the changepoint analysis.0% of anomalies were detected as outliers and 0 of anomalies were detected in the changepoint analysis.

- -

plot of chunk unnamed-chunk-7

- -

The more stable region selected consistent for all channels is highlighted in yellow. If the removal of outliers has been required before the execution of the changepoint analysis, the detected outliers are cicled in green.

- -

The FCS file was divided in 100 bins. The stable region is located between the bins 1 and 100.

- -

More info on the changepoints detected:

- -

No changepoints were detected.

- -

Channels excluded from the analysis: FSC-H, SSC-H.

- -

No changepoints were detected in the channels: FL1-H, FL2-H, FL3-H, FL4-H.

- -

Dynamic range check

- -

-
25.11 % anomalies detected in dynamic range check.
-

- -

plot of chunk unnamed-chunk-11

- -

The plot shows where the anomalies occured the most. The x-axis scale is complementary to the one of the signal acquisition plot.

- -

More info on the anomalies detected in the dynamic range check:

- -

for each channel, The table shows the number of events that did not pass the dynamic range check:

- -

##              lower_range upper_range
-## FSC-H                  0         217
-## SSC-H                  0        4990
-## FL1-H                  0           0
-## FL2-H                  0           0
-## FL3-H                  0           0
-## FL4-H                  0           0
-## total_SUM              0        5207
-## total_UNIQUE           0        5022
-

- - - - diff -r 60aa5e56531a -r 34397a84faf1 flowai/test-data/nooutliers/hqdata_nooutliers.fcs Binary file flowai/test-data/nooutliers/hqdata_nooutliers.fcs has changed diff -r 60aa5e56531a -r 34397a84faf1 flowai/test-data/std/QCreport.html --- a/flowai/test-data/std/QCreport.html Mon Feb 27 12:55:30 2017 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,238 +0,0 @@ - - - - - -FCS file information - - - - - - - - - - - - - - -

FCS file information

- -

-
Input file name: dataset_934
-Number of events: 20000
-

- -

Quality control analysis

- -

Summary

- -

-
The anomalies were removed from: Flow Rate, Flow Signal and Flow Margin
-Anomalies detected in total: 25.11 %
-Number of high quality events: 14978
-

- -

Flow rate check

- -

-
0 % anomalies detected in the flow rate check.
-

- -

It was not possible to analyze the flow rate since the time channel is missing.

- -

Signals acquisition check

- -

-
0 % anomalies detected in the signal aquisition check.
-

- -

plot of chunk unnamed-chunk-7

- -

The FCS file was divided in 100 bins. The stable region is located between the bins 1 and 100.

- -

More info on the changepoints detected:

- -

No changepoints were detected.

- -

Channels excluded from the analysis: FSC-H, SSC-H.

- -

No changepoints were detected in the channels: FL1-H, FL2-H, FL3-H, FL4-H.

- -

Dynamic range check

- -

-
25.11 % anomalies detected in dynamic range check.
-

- -

plot of chunk unnamed-chunk-11

- -

The plot shows where the anomalies occured the most. The x-axis scale is complementary to the one of the signal acquisition plot.

- -

More info on the anomalies detected in the dynamic range check:

- -

for each channel, The table shows the number of events that did not pass the dynamic range check:

- -

##              lower_range upper_range
-## FSC-H                  0         217
-## SSC-H                  0        4990
-## FL1-H                  0           0
-## FL2-H                  0           0
-## FL3-H                  0           0
-## FL4-H                  0           0
-## total_SUM              0        5207
-## total_UNIQUE           0        5022
-

- - - - diff -r 60aa5e56531a -r 34397a84faf1 flowai/test-data/std/alldata.fcs Binary file flowai/test-data/std/alldata.fcs has changed diff -r 60aa5e56531a -r 34397a84faf1 flowai/test-data/std/hqdata.fcs Binary file flowai/test-data/std/hqdata.fcs has changed diff -r 60aa5e56531a -r 34397a84faf1 flowai/test-data/std/lqdata.fcs Binary file flowai/test-data/std/lqdata.fcs has changed diff -r 60aa5e56531a -r 34397a84faf1 flowai/test-data/withsfsc/QCreport_sfsc.html --- a/flowai/test-data/withsfsc/QCreport_sfsc.html Mon Feb 27 12:55:30 2017 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,236 +0,0 @@ - - - - - -FCS file information - - - - - - - - - - - - - - -

FCS file information

- -

-
Input file name: dataset_934
-Number of events: 20000
-

- -

Quality control analysis

- -

Summary

- -

-
The anomalies were removed from: Flow Rate, Flow Signal and Flow Margin
-Anomalies detected in total: 25.11 %
-Number of high quality events: 14978
-

- -

Flow rate check

- -

-
0 % anomalies detected in the flow rate check.
-

- -

It was not possible to analyze the flow rate since the time channel is missing.

- -

Signals acquisition check

- -

-
0 % anomalies detected in the signal aquisition check.
-

- -

plot of chunk unnamed-chunk-7

- -

The FCS file was divided in 100 bins. The stable region is located between the bins 1 and 100.

- -

More info on the changepoints detected:

- -

No changepoints were detected.

- -

No changepoints were detected in the channels: FSC-H, SSC-H, FL1-H, FL2-H, FL3-H, FL4-H.

- -

Dynamic range check

- -

-
25.11 % anomalies detected in dynamic range check.
-

- -

plot of chunk unnamed-chunk-11

- -

The plot shows where the anomalies occured the most. The x-axis scale is complementary to the one of the signal acquisition plot.

- -

More info on the anomalies detected in the dynamic range check:

- -

for each channel, The table shows the number of events that did not pass the dynamic range check:

- -

##              lower_range upper_range
-## FSC-H                  0         217
-## SSC-H                  0        4990
-## FL1-H                  0           0
-## FL2-H                  0           0
-## FL3-H                  0           0
-## FL4-H                  0           0
-## total_SUM              0        5207
-## total_UNIQUE           0        5022
-

- - - - diff -r 60aa5e56531a -r 34397a84faf1 flowai/test-data/withsfsc/hqdata_sfsc.fcs Binary file flowai/test-data/withsfsc/hqdata_sfsc.fcs has changed diff -r 60aa5e56531a -r 34397a84faf1 static/images/flowtools/autoflowrate.png Binary file static/images/flowtools/autoflowrate.png has changed diff -r 60aa5e56531a -r 34397a84faf1 static/images/flowtools/autosignal.png Binary file static/images/flowtools/autosignal.png has changed diff -r 60aa5e56531a -r 34397a84faf1 static/images/flowtools/margins.png Binary file static/images/flowtools/margins.png has changed diff -r 60aa5e56531a -r 34397a84faf1 test-data/input.fcs Binary file test-data/input.fcs has changed diff -r 60aa5e56531a -r 34397a84faf1 test-data/nooutliers/QCreport_nooutliers.html --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/nooutliers/QCreport_nooutliers.html Tue Jun 23 18:34:02 2020 -0400 @@ -0,0 +1,240 @@ + + + + + +FCS file information + + + + + + + + + + + + + + +

FCS file information

+ +

+
Input file name: dataset_934
+Number of events: 20000
+

+ +

Quality control analysis

+ +

Summary

+ +

+
The anomalies were removed from: Flow Rate, Flow Signal and Flow Margin
+Anomalies detected in total: 25.11 %
+Number of high quality events: 14978
+

+ +

Flow rate check

+ +

+
0 % anomalies detected in the flow rate check.
+

+ +

It was not possible to analyze the flow rate since the time channel is missing.

+ +

Signals acquisition check

+ +

+
0 % anomalies detected in the signal aquisition check.
+

+ +

Outliers were removed before the changepoint analysis.0% of anomalies were detected as outliers and 0 of anomalies were detected in the changepoint analysis.

+ +

plot of chunk unnamed-chunk-7

+ +

The FCS file was divided in 100 bins. The stable region is located between the bins 1 and 100.

+ +

More info on the changepoints detected:

+ +

No changepoints were detected.

+ +

Channels excluded from the analysis: FSC-H, SSC-H.

+ +

No changepoints were detected in the channels: FL1-H, FL2-H, FL3-H, FL4-H.

+ +

Dynamic range check

+ +

+
25.11 % anomalies detected in dynamic range check.
+

+ +

plot of chunk unnamed-chunk-11

+ +

The plot shows where the anomalies occured the most. The x-axis scale is complementary to the one of the signal acquisition plot.

+ +

More info on the anomalies detected in the dynamic range check:

+ +

for each channel, The table shows the number of events that did not pass the dynamic range check:

+ +

##              lower_range upper_range
+## FSC-H                  0         217
+## SSC-H                  0        4990
+## FL1-H                  0           0
+## FL2-H                  0           0
+## FL3-H                  0           0
+## FL4-H                  0           0
+## total_SUM              0        5207
+## total_UNIQUE           0        5022
+

+ + + + diff -r 60aa5e56531a -r 34397a84faf1 test-data/nooutliers/hqdata_nooutliers.fcs Binary file test-data/nooutliers/hqdata_nooutliers.fcs has changed diff -r 60aa5e56531a -r 34397a84faf1 test-data/std/QCreport.html --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/std/QCreport.html Tue Jun 23 18:34:02 2020 -0400 @@ -0,0 +1,238 @@ + + + + + +FCS file information + + + + + + + + + + + + + + +

FCS file information

+ +

+
Input file name: dataset_934
+Number of events: 20000
+

+ +

Quality control analysis

+ +

Summary

+ +

+
The anomalies were removed from: Flow Rate, Flow Signal and Flow Margin
+Anomalies detected in total: 25.11 %
+Number of high quality events: 14978
+

+ +

Flow rate check

+ +

+
0 % anomalies detected in the flow rate check.
+

+ +

It was not possible to analyze the flow rate since the time channel is missing.

+ +

Signals acquisition check

+ +

+
0 % anomalies detected in the signal aquisition check.
+

+ +

plot of chunk unnamed-chunk-7

+ +

The FCS file was divided in 100 bins. The stable region is located between the bins 1 and 100.

+ +

More info on the changepoints detected:

+ +

No changepoints were detected.

+ +

Channels excluded from the analysis: FSC-H, SSC-H.

+ +

No changepoints were detected in the channels: FL1-H, FL2-H, FL3-H, FL4-H.

+ +

Dynamic range check

+ +

+
25.11 % anomalies detected in dynamic range check.
+

+ +

plot of chunk unnamed-chunk-11

+ +

The plot shows where the anomalies occured the most. The x-axis scale is complementary to the one of the signal acquisition plot.

+ +

More info on the anomalies detected in the dynamic range check:

+ +

for each channel, The table shows the number of events that did not pass the dynamic range check:

+ +

##              lower_range upper_range
+## FSC-H                  0         217
+## SSC-H                  0        4990
+## FL1-H                  0           0
+## FL2-H                  0           0
+## FL3-H                  0           0
+## FL4-H                  0           0
+## total_SUM              0        5207
+## total_UNIQUE           0        5022
+

+ + + + diff -r 60aa5e56531a -r 34397a84faf1 test-data/std/alldata.fcs Binary file test-data/std/alldata.fcs has changed diff -r 60aa5e56531a -r 34397a84faf1 test-data/std/hqdata.fcs Binary file test-data/std/hqdata.fcs has changed diff -r 60aa5e56531a -r 34397a84faf1 test-data/std/lqdata.fcs Binary file test-data/std/lqdata.fcs has changed diff -r 60aa5e56531a -r 34397a84faf1 test-data/withsfsc/QCreport_sfsc.html --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/withsfsc/QCreport_sfsc.html Tue Jun 23 18:34:02 2020 -0400 @@ -0,0 +1,236 @@ + + + + + +FCS file information + + + + + + + + + + + + + + +

FCS file information

+ +

+
Input file name: dataset_934
+Number of events: 20000
+

+ +

Quality control analysis

+ +

Summary

+ +

+
The anomalies were removed from: Flow Rate, Flow Signal and Flow Margin
+Anomalies detected in total: 25.11 %
+Number of high quality events: 14978
+

+ +

Flow rate check

+ +

+
0 % anomalies detected in the flow rate check.
+

+ +

It was not possible to analyze the flow rate since the time channel is missing.

+ +

Signals acquisition check

+ +

+
0 % anomalies detected in the signal aquisition check.
+

+ +

plot of chunk unnamed-chunk-7

+ +

The FCS file was divided in 100 bins. The stable region is located between the bins 1 and 100.

+ +

More info on the changepoints detected:

+ +

No changepoints were detected.

+ +

No changepoints were detected in the channels: FSC-H, SSC-H, FL1-H, FL2-H, FL3-H, FL4-H.

+ +

Dynamic range check

+ +

+
25.11 % anomalies detected in dynamic range check.
+

+ +

plot of chunk unnamed-chunk-11

+ +

The plot shows where the anomalies occured the most. The x-axis scale is complementary to the one of the signal acquisition plot.

+ +

More info on the anomalies detected in the dynamic range check:

+ +

for each channel, The table shows the number of events that did not pass the dynamic range check:

+ +

##              lower_range upper_range
+## FSC-H                  0         217
+## SSC-H                  0        4990
+## FL1-H                  0           0
+## FL2-H                  0           0
+## FL3-H                  0           0
+## FL4-H                  0           0
+## total_SUM              0        5207
+## total_UNIQUE           0        5022
+

+ + + + diff -r 60aa5e56531a -r 34397a84faf1 test-data/withsfsc/hqdata_sfsc.fcs Binary file test-data/withsfsc/hqdata_sfsc.fcs has changed