Drawing Pedigree Charts from Simple Text Descriptions
Pedigree charts are used in Medicine to record a patient’s family history. They are particularly useful to document genetic diseases that can be inherited from one generation to the next. The example below shows a pedigree chart of a (fictitious) family where multiple individuals are affected by breast cancer:
In most clinical settings, pedigree charts are still drawn by hand on paper, which limits their utility. Pedigree drawing software tools exist but are complicated to use and/or record their data in proprietary formats that are unsuitable for medical research purposes.
In this project, we aim to develop a pedigree drawing engine that can create pedigree charts as the example above from simple textual descriptions. The concept is similar to Graphviz (https://www.graphviz.org/) and mermaid (https://mermaidjs.github.io/), two projects that allow creating graphs and diagrams using a simple text syntax.
There are currently two ways to access the TXT2PED:
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Directly access through web:
(Maybe not able to access due to limit active policy on shinyapps.io (we were using a free account). ) https://6112project.shinyapps.io/Pedigree_project/
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Clone the repo and run the shiny.R in Rstudio.
To be able to use this pedigree engine, R need to be installed. To have a better experience, python3 will be required to install. Python wil auto install any needed python package. But R module kinship2 needed manual install. To install kinship 2 use command 'install.packages('kinship 2') in R console.
Python version was no longer in develop
using command below will generate graph:
- A father_of C,D,F
- B partner_of A
- E father_of G,I,J
- H partner_of E
- F father_of Z,V
- G mother_of Z,V
- C,D,I gender_is male
- J,Z,V gender_is female
- A,C,F,Z,V affected_is diseaseA
- E,G,Z affected_is diseaseB
- Z d_twin V
Affected attribute must be assign at last or after creating every nodes otherwise an error will rise.
More example input can be found in the sampleinput folder.
Affected attributes should be define after all nodes has been created
- A gender_is male
- A,B,C gender_is female
- A name_is "John Doe"
- A DOB_is "13 Oct 1970"
- A affect_is diseaseA
- A deceased_is true
- A,B,C deceased_is true
- A affected_is diseaseA,B,C
- A,B,C affected_is diseaseX,Y,Z
- A ad_is "additional text""
- A father_of B
- A father_of B,C,D
- A mother_of B
- A mother_of B,C,D
- A partner_of B
- A m_twin B
- A d_twin B
- A unkonwn_twin B
Sequence of input is important. Different sequence of input may result in different graph.
Twin relation and Affected attribute must be assigned at last or after creating every node otherwise an error will rise.
TO FIND More help plz find documentation in the REPO