# HG changeset patch # User immport-devteam # Date 1488218130 18000 # Node ID 60aa5e56531a7d0d7ac6e4231003a6a4af5c0f70 Uploaded diff -r 000000000000 -r 60aa5e56531a flowai/FCSflowAI.R --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/flowai/FCSflowAI.R Mon Feb 27 12:55:30 2017 -0500 @@ -0,0 +1,41 @@ +# +# +# 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 000000000000 -r 60aa5e56531a flowai/FCSflowAI.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/flowai/FCSflowAI.xml Mon Feb 27 12:55:30 2017 -0500 @@ -0,0 +1,178 @@ + + automatic quality control + + r + bioconductor-flowcore + bioconductor-flowai + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + (highQ_FCS) + + + (lowQ_FCS) + + + (QC_FCS) + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 10.1093/bioinformatics/btw191 + + diff -r 000000000000 -r 60aa5e56531a flowai/static/images/flowtools/autoflowrate.png Binary file flowai/static/images/flowtools/autoflowrate.png has changed diff -r 000000000000 -r 60aa5e56531a flowai/static/images/flowtools/autosignal.png Binary file flowai/static/images/flowtools/autosignal.png has changed diff -r 000000000000 -r 60aa5e56531a flowai/static/images/flowtools/margins.png Binary file flowai/static/images/flowtools/margins.png has changed diff -r 000000000000 -r 60aa5e56531a flowai/test-data/input.fcs Binary file flowai/test-data/input.fcs has changed diff -r 000000000000 -r 60aa5e56531a flowai/test-data/nooutliers/QCreport_nooutliers.html --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/flowai/test-data/nooutliers/QCreport_nooutliers.html Mon Feb 27 12:55:30 2017 -0500 @@ -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 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 000000000000 -r 60aa5e56531a flowai/test-data/nooutliers/hqdata_nooutliers.fcs Binary file flowai/test-data/nooutliers/hqdata_nooutliers.fcs has changed diff -r 000000000000 -r 60aa5e56531a flowai/test-data/std/QCreport.html --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/flowai/test-data/std/QCreport.html Mon Feb 27 12:55:30 2017 -0500 @@ -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 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 000000000000 -r 60aa5e56531a flowai/test-data/std/alldata.fcs Binary file flowai/test-data/std/alldata.fcs has changed diff -r 000000000000 -r 60aa5e56531a flowai/test-data/std/hqdata.fcs Binary file flowai/test-data/std/hqdata.fcs has changed diff -r 000000000000 -r 60aa5e56531a flowai/test-data/std/lqdata.fcs Binary file flowai/test-data/std/lqdata.fcs has changed diff -r 000000000000 -r 60aa5e56531a flowai/test-data/withsfsc/QCreport_sfsc.html --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/flowai/test-data/withsfsc/QCreport_sfsc.html Mon Feb 27 12:55:30 2017 -0500 @@ -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 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.

+ +

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 000000000000 -r 60aa5e56531a flowai/test-data/withsfsc/hqdata_sfsc.fcs Binary file flowai/test-data/withsfsc/hqdata_sfsc.fcs has changed