### configuration file for GO::View module and batchGOView.pl
######################################################################
## Note that paths in this file that are not absolute, ie don't begin
## with a slash, are interpreted as relative to THIS file.
## to define the maximum number of the nodes to be displayed in the map.
maxNode = 30
## to define the minimum map width
minMapWidth = 350
## to define the minimum map height for displaying keys on the top
minMapHeight4TopKey = 600
## to define the minimum map width for displaying keys on a single row
minMapWidth4OneLineKey = 620
## to define the display ratio of the map width over the width defined
## by GraphViz module
widthDisplayRatio = 0.8
## to define the display ratio of the map height over the height
## defined by GraphViz module
heightDisplayRatio = 0.8
## The 'dot' and 'neato' are located under this directory. Just delete
## this entry if you have installed the dot and neato programs under
## default directory.
binDir =
## The required C libraries for dot and neato are located under this
## directory. Just delete this entry if you have installed these
## libraries under default directory.
libDir =
## the note will be displayed on the bottom of the map
## see example below:
## mapNote = general map note here
mapNote =
## the annotation file that you want to use for the example run of
## batchGOView.pl, it is indicated to be the test one in the ../t/
## directory. Note that this is only for illustrative purposes - that
## file is old, and you should get the latest ones from the Gene
## Ontology Consortium for your own purposes.
annotationFile = ../t/gene_association.sgd
## the ontology file - see notes on association file
ontologyFile = ../t/gene_ontology_edit.obo
## aspect - the aspect of the ontology
aspect = P
## totalNumGenes - the total number of genes that were assayed in the
## course of determining interesting ones. If this is left blank,
## then it is assumed that this number is the same as the number of
## genes in the annotation file
totalNumGenes =
## outDir - the output directory, where you want the resulting html
## files to be put. default is to output them to the same directory
## as the .conf file
outDir =
## geneUrl - a url to which you want your genes linked in both the
## image and the html table It must have the text <REPLACE_THIS> which
## will be replaced with the gene name
geneUrl = http://db.yeastgenome.org/cgi-bin/SGD/locus.pl?locus=<REPLACE_THIS>
## goidUrl - a url to which you want your GO nodes linked in both the
## image and the html table It must have the text <REPLACE_THIS> which
## will be replaced with the gene name
goidUrl = http://amigo.geneontology.org/cgi-bin/amigo/go.cgi?view=details&search_constraint=terms&depth=0&query=<REPLACE_THIS>
## pvaluecutoff - the p-value cutoff, above which you do not want
## genes printed out to the html table. If none is provided, or you
## provde a zero, then a value of 1 will be used (ie no cutoff)
pvalueCutOff = 0.01
## calculateFDR - boolean to decide whether the FDR should be
## calculated when the terms are found for the list of genes. If no
## value is provided then the default for GO::TermFinder will be used,
## which is 0 (i.e. to not calculate the FDR).
calculateFDR = 1
## makePs - boolean to decided whether, in addition to a png or gif
## image (depending on the version of GD you are using), a postscript
## should also be created. The postscript image will have the same
## name as the png/gif image, but will have a different suffix. Note
## that because I don't seem to be able to get the postcript options
## to work completely correctly, opting for postscript currently
## constrains the size of your images, including the png/gif ones.
## Still, it does give you nice scaleable output for publication.
##
## 0 means no ps, 1 means you should get an image
makePs = 0