Madeline: pedigree drawing with an emphasis on readability and aesthetics.

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The Madeline 2.0 Pedigree Drawing Engine (PDE) is a pedigree drawing program for use in linkage and family-based association studies. The program is designed to handle large and complex pedigrees with an emphasis on readability and aesthetics.

References:

Edward H. Trager, Ritu Khanna, Adrian Marrs, Lawrence Siden, Kari E.H. Branham, Anand Swaroop and Julia E. Richards,
Madeline 2.0 PDE: a new program for local and web-based pedigree drawing.
Bioinformatics, 2007, 23(14), pp. 1854–1856.

Documentation

Important Notes

Module Name: Madeline (see the modules page for more information)
Unusual environment variables set
- MADELINE_HOME MADELINE installation directory
- MADELINE_BIN MADELINE executable directory
- MADELINE_SRC MADELINEsource code directory
- MADELINE_DATA MADELINE sample data directory

Interactive job

Interactive jobs should be used for debugging, graphics, or applications that cannot be run as batch jobs.

Allocate an interactive session and run the program. Sample session:

[user@biowulf]$ sinteractive 
[user@cn0849 ~]$ module load Madeline 
[+] Loading madeline  2.0  on cn0849
[+] Loading singularity  3.8.5-1  on cn0849
[+] Loading ImageMagick  7.0.7  on cn0849

Copy test data to your current filder:

[user@cn0849 ~]$ cp -r $MADELINE_DATA/* .

Run the madeline executable on the test data:

[user@cn0849 ~]$ madeline -L "IndividualID DOB" ./input/si_001.data
┌─────────────────────────────┐
│ Welcome to Madeline 2.0 PDE │
└─────────────────────────────┘
--------------------------------------------
 LABELS                          TOTAL: 2
--------------------------------------------
 1. IndividualID
 2. DOB
--------------------------------------------
Parser::readFile(): Opening a(n) UTF-8 file ...
Reading file data in Madeline flat file format ...
----------------------------------------------------------------
 ICON COLUMNS                                        TOTAL: 1
----------------------------------------------------------------
   1. Affected                         has 2 non-missing levels.
----------------------------------------------------------------
Table 1 is a pedigree table.
  Start of    addPedigreesFromDataTable 
Warning: Adding virtual father “S00100” who is not present in the input data file.
Warning: Adding virtual mother “S00101” who is not present in the input data file.
Siblings are ordered by DOB.
  End of      addPedigreesFromDataTable 
  Start of    draw                       
Pedigree output file is “si_001_pedigree.svg”
  End of      draw                       

[user@cn0849 ~]$ madeline --color ./input/si_002.data
┌─────────────────────────────┐
│ Welcome to Madeline 2.0 PDE │
└─────────────────────────────┘
--------------------------------------------
 LABELS                          TOTAL: 0
--------------------------------------------
--------------------------------------------
Parser::readFile(): Opening a(n) UTF-8 file ...
Reading file data in Madeline flat file format ...
----------------------------------------------------------------
 ICON COLUMNS                                        TOTAL: 1
----------------------------------------------------------------
   1. Affected                         has 3 non-missing levels.
----------------------------------------------------------------
Table 1 is a pedigree table.
  Start of    addPedigreesFromDataTable  
Siblings are ordered by DOB.
  End of      addPedigreesFromDataTable  
  Start of    draw                       
Pedigree output file is “si_002_pedigree.svg”
  End of      draw

Visualize the results:

[user@cn0849 ~]$ display si_001_pedigree.svg

[user@cn0849 ~]$ display si_002_pedigree.svg

[user@cn0849 ~]$ exit exit salloc.exe: Relinquishing job allocation 28896415 salloc.exe: Job allocation 28896415 has been revoked. [user@biowulf ~]$