indRender: indented textual rendering of nodes of a hierarchical graph
In keggorthology: graph support for KO, KEGG Orthology

Description Usage Arguments Details Value Author(s) Examples

View source: R/indRender.R

indented textual rendering of nodes of a hierarchical graph

1	indRender(klike, from=nodes(klike)[1], indent=" ")

`klike`	a graph, with tree structure similar to `KOgraph`
`from`	a node name from which the rendering should proceed to all leaves
`indent`	token to use for indentation – will be replicated to depth of node to be rendered to its left

Based on keggorthology read of KEGG orthology, March 2 2010. Specifically, we run wget on ftp://ftp.genome.jp/pub/kegg/brite/ko/ko00001.keg and use parsing and modeling code given in inst/keggHTML to generate a data frame respecting the hierarchy, and then keggDF2graph to construct the graph.

NULL

Vince Carey <stvjc@channing.harvard.edu>

1 2	data(KOgraph) indRender(KOgraph, "Human Diseases")

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    Cancers 
      Pathways in cancer 
      Colorectal cancer 
      Pancreatic cancer 
      Glioma 
      Thyroid cancer 
      Acute myeloid leukemia 
      Chronic myeloid leukemia 
      Basal cell carcinoma 
      Melanoma 
      Renal cell carcinoma 
      Bladder cancer 
      Prostate cancer 
      Endometrial cancer 
      Small cell lung cancer 
      Non-small cell lung cancer 
    Immune System Diseases 
      Asthma 
      Systemic lupus erythematosus 
      Autoimmune thyroid disease 
      Allograft rejection 
      Graft-versus-host disease 
      Primary immunodeficiency 
    Neurodegenerative Diseases 
      Alzheimer's disease 
      Parkinson's disease 
      Amyotrophic lateral sclerosis (ALS) 
      Huntington's disease 
      Prion diseases 
    Circulatory Diseases 
      Hypertrophic cardiomyopathy (HCM) 
      Arrhythmogenic right ventricular cardiomyopathy (ARVC) 
      Dilated cardiomyopathy (DCM) 
      Viral myocarditis 
    Metabolic Diseases 
      Type I diabetes mellitus 
      Type II diabetes mellitus 
      Maturity onset diabetes of the young 
    Infectious Diseases 
      Vibrio cholerae infection 
      Vibrio cholerae pathogenic cycle 
      Epithelial cell signaling in Helicobacter pylori infection 
      Pathogenic Escherichia coli infection