Program: HAPPI Description: Hyperlinked Analysis of Protein-Protein Interactions Version: 1.2 Last Edit: 06/03/13 Citation: Edwards et al. (2011), Molecular Biosystems DOI: 10.1039/C1MB05212H.

Copyright © 2010 Richard J. Edwards - See source code for GNU License Notice

Imported modules: rje rje_db rje_go rje_html rje_ppi rje_sequence rje_slim rje_uniprot rje_zen rje_dismatrix_V2 rje_tree

See SLiMSuite Blog for further documentation. See rje for general commands.

Function

This module makes a set of linked webpages for the quick and dirty analysis of PPI networks around one or more sets of genes. A table of genes and their corresponding classes is used to make the initial front page tables.

Additional data tables can also be loaded and linked via the "Gene" field for individual Gene Pages. These must be named in the format X.N.tdt, where N will be used as the tab name.

Additional classes can be added using the makeclass and classorder lists. Any classes in classorder that are not found in indata will be added using the rules set by makeclass: - go = GO term description or ID - keyword = found in GO term description or protein description - desc = found in protein description - xref = adds PPI for protein identified from xrefdata table - add = will only add a gene to a class if it does not already have one (no multiple-class genes)

Commandline

INPUT

indata=FILE : Input data for front pages []
pagehead=X : Text for Front Page Header ['HAPPI Analysis of basefile']
infotext=X : Text to display under header ['This data has not yet been published and should not be used without permission.']
genefield=X : Field to be used for indentifying Genes ['Gene']
geneclass=X : Field used to identify class of Genes ['Class']
classcol=X : Table of "Class" and "Col" (soton$col indexes) to be used for PPI images [basefile.col.tdt]
fillcol=T/F : Fill in colour for missing class combinations [True]
classorder=LIST : List of Class orders (otherwise alphabetical) []
multiclass=T/F : Whether to allow membership of multiple classes (joined by "-" [True]
makeclass=LIST : Generate classes from classorder LIST if missing from indata (go/keyword/desc/xref(+ppi)/add*) [keyword]
genedata=LIST : List of additional data tables for Gene-centric pages. Must have "Gene" or genefield field. []
xrefdata=FILE : File of Database cross-references. Must have "Gene" field. []
xreftab=T/F : Add database cross-reference tabs to the front page Class tabs [True]
pairwise=FILE : Pairwise protein-protein interation (PPI) file []
addppi=LIST : List of additional PPI pairwise files to add []
addclass=T/F : Whether to add the Classes themselves to the PPI networks as nodes [False]
godata=FILE : Delimited file of GO Data (Gene,GO_ID,GO_Type,GO_Desc) [basefile.go.tdt]
gablam=FILE : Delimited GABLAM results file for homology data [basefile.gablam.tdt]
ppexpand=X : Expand PPI by X levels for MCODE complex generation [1]
ppcomplex=LIST : List of different evidence codes for special MCODE analyses ['Complex']
ppextra=T/F : Make additional pages for genes added and returned in MCODE clusters [False]
combine=LIST : List of Classes to combine into Interactome for front page ('all' or '*' for all) []
special=LIST : Execute special analysis code for specific applications []

BASIC OUTPUT OPTIONS

htmlpath=PATH : Path of parent html directory [./html]
stylesheets=LIST : List of CSS files to use ['../example.css','../redwards.css']
border=X : Border setting for tables [0]
dropfields=LIST : Fields to exclude from summary tables []
makepng=T/F : Whether to (look for and) make PNG files with R [True]
pngmax=X : Max number of genes for PNG construction [2000]
svg=T/F : Use SVG files instead of PNG files [True]
xgmml=T/F : Whether to also output XGMML files in PNG/SVG directories [False]
makepages=LIST : Types of pages to make [front,gene,go,mcode,class,interactome,expand]
titletext=FILE : File containing (Page,ID,Title) for mouseover text [titletext.tdt]
gopages=X : Create Pages of GO terms with X+ representative genes [5]
maxgo=X : Go terms above X genes will not have gene data tabs [500]
nobots=T/F : Whether to insert no-bot meta tag to pages [True]

FIGURE REMAKING OPTIONS

usepos=T/F : Whether to use existing Node positions if found [True]
updatepos=T/F : Whether to run an additional round of the layout algorithm if npos found [False]
* See also RJE_PPI Fragment and MCODE options *
* See also RJE_GO options *

See also rje.py generic commandline options.

History Module Version History

    # 0.0 - Initial Compilation. Based on rje_hm_html.
    # 0.1 - Added special methods for specific analyses.
    # 0.2 - Added multiclass capability.
    # 0.3 - Added GO enrichment to MCODE complexes.
    # 0.4 - Added "expanded" MCODE complex and updated GO enrichment of complexes.
    # 0.5 - Added class colour compilation.
    # 0.6 - Replaced ppcomplex=T/F with list of different evidence codes for special MCODE analyses ['Complex']
    # 0.7 - Added ppextra option for adding additional pages for genes added and returned in MCODE clusters.
    # 0.8 - Added use of SVG PPI images in place of PNG.
    # 0.9 - Added GZipping of XGMML files to save space.
    # 1.0 - Fixed PNG/SVG XGMML directory issue. First release.
    # 1.1 - Fixed SVG class naming issue (Cannot have *.class.svg!)
    # 1.2 - Added addclass and refined output for Host-Pathogen PPI analysis.