run.som <- function(modpar=modpar,modsom=modsom)
{
#library(oposSOM)
#library(igraph)
#library(ape)
#library(tsne)
#library(som)
#library(fastICA)
#source("multiSOMe.r")
env <- opossom.new(list(dataset.name = paste(modpar$dataset.name,modpar$weight,sep="_"),
dim.1stLvlSom = modpar$dim.1stLvlSom,
dim.2ndLvlSom = 20,
training.extension = 1,
rotate.SOM.portraits = 0,
flip.SOM.portraits = F,
database.biomart = modpar$database.biomart,
database.host = modpar$database.host,
database.dataset = modpar$database.dataset,
database.id.type =modpar$return.ids,
activated.modules = list( "reporting" = TRUE,
"primary.analysis" = TRUE,
"sample.similarity.analysis" = TRUE,
"geneset.analysis" = modpar$geneset.analysis,
"geneset.analysis.exact" = FALSE,
"group.analysis" = TRUE,
"difference.analysis" = TRUE ),
standard.spot.modules = "dmap",
spot.coresize.modules = 3,
spot.threshold.modules = 0.95,
spot.coresize.groupmap = 3,
spot.threshold.groupmap = 0.75,
feature.centralization = F,
sample.quantile.normalization = F,
pairwise.comparison.list = list() ) )
# Load input data
env$indata <-modsom$indata
# Define sample groups
env$group.labels <- modsom$group.labels
if(exists("group.colors"))
env$group.colors <- group.colors
multiSOMe.run(env)
eachOME.run(env)
}
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