inst/unitTests/test_NetworkView.R

In PriceLab/TrenaViz: TrenaViz

library(TrenaViz)
library(RUnit)
library(graph)

if(!exists("tv")){
   tv <- TrenaViz("TrenaProjectLymphocyte")
   tp <- TrenaProjectLymphocyte()
   load("gata2.model.RData")
   }
#------------------------------------------------------------------------------------------------------------------------
runTests <- function()
{
   test_.standardizeModelTable()
   test_.standardizeRegulatoryRegionsTable()
   test_.geneRegulatoryModelToGraph()
   test_.addGeneModelLayout()

} # runTests
#------------------------------------------------------------------------------------------------------------------------
test_.standardizeModelTable <- function()
{
   printf("--- test_.standardizeModelTable")

   #-----------------------------------------------------------------------------------------
   # the incoming tbl.model presents these challenges:
   #
   #       gene betaLasso  lassoPValue pearsonCoeff  rfScore   betaRidge spearmanCoeff bindingSites
   #  6    E2F3         0 7.124847e-07    0.8683105 2.936714  0.04945335     0.8149973           NA
   #  45 HOXC13         0 3.987483e-02   -0.8640875 2.457541 -0.01531601    -0.7659080           NA
   #  97 ZNF263         0 6.236969e-01    0.9003067 2.134046  0.04104303     0.6360153           NA
   #  70  PRDM4         0 1.000000e+00    0.8984506 1.900193  0.03627523     0.7405583           NA
   #
   # and for which we want these results (first 4 rows only)
   #
   #         tf    pearson   spearman betaLasso randomForest
   #  6    E2F3  0.8683105  0.8149973         0     2.936714
   #  45 HOXC13 -0.8640875 -0.7659080         0     2.457541
   #  97 ZNF263  0.9003067  0.6360153         0     2.134046
   #  70  PRDM4  0.8984506  0.7405583         0     1.900193

   tbl.std <- TrenaViz:::.standardizeModelTable(tbl.model)
   checkEquals(dim(tbl.std), c(nrow(tbl.model), 5))
   checkEquals(colnames(tbl.std), c("tf", "pearson", "spearman", "betaLasso", "randomForest"))
   checkEquals(tbl.model$gene, tbl.std$tf)
   checkEquals(tbl.model$rfScore, tbl.std$randomForest)

} # test_.standardizeModelTable
#------------------------------------------------------------------------------------------------------------------------
test_.standardizeRegulatoryRegionsTable <- function()
{
   printf("--- test_.standardizeRegulatoryRegionsTable")

   tbl.regions <- get(load("../extdata/tbl.regRegions-GATA2.RData"))
   library(TrenaProjectErythropoiesis)
   tp <- TrenaProjectErythropoiesis()
   tss <- getTranscriptsTable(tp, "GATA2")$start
   targetGene <- "GATA2"
   tbl.std <- TrenaViz:::.standardizeRegulatoryRegionsTable(tbl.regions, targetGene, tss)
   checkEquals(nrow(tbl.regions), nrow(tbl.std))
   checkEquals(tbl.regions$geneSymbol, tbl.std$tf)
   checkEquals(tbl.regions$fp_start, tbl.std$start)
   checkTrue(all(tbl.std$targetGene == targetGene))

} # test_.standardizeRegulatoryRegionsTable
#------------------------------------------------------------------------------------------------------------------------
test_.geneRegulatoryModelToGraph <- function()
{
   printf("--- test_.geneRegulatoryModelToGraph")

   f <- system.file(package="TrenaViz", "extdata", "model.and.regRegions.irf4.top5.RData")
   print(load(f))

   targetGene <- "IRF4"
   tss <- getTranscriptsTable(tp, targetGene)$start
   g <- TrenaViz:::.geneRegulatoryModelToGraph(targetGene, tss, tbl.model, tbl.reg)

   checkEquals(sort(names(nodeDataDefaults(g))), c("betaLasso",   "distance",    "label",
                                                   "motif",       "pearson",     "randomForest",
                                                   "type",        "xPos",        "yPos"))
   checkEquals(sort(names(edgeDataDefaults(g))), "edgeType")
   checkEquals(length(nodes(g)), 13)
   checkEquals(length(names(edgeData(g, attr="edgeType"))), 14)
   expected.nodes <- c("IRF4", "IRF4:-51:PAX5", "IRF4:-76:MGA", "IRF4:1320:ZBTB4", "IRF4:1819:MAF",
                       "IRF4:1986:MGA", "IRF4:295:MGA", "IRF4:397:RFX5", "MAF", "MGA", "PAX5", "RFX5", "ZBTB4")
   checkEquals(sort(nodes(g)), expected.nodes)
   checkEquals(sort(unique(unlist(edgeData(g, attr="edgeType"), use.names=FALSE))),
               c("bindsTo", "regulatorySiteFor"))
   expected.edgeNames <- c("IRF4:-51:PAX5|IRF4",   "IRF4:-76:MGA|IRF4",
                           "IRF4:1320:ZBTB4|IRF4", "IRF4:1819:MAF|IRF4",
                           "IRF4:1986:MGA|IRF4",   "IRF4:295:MGA|IRF4",
                           "IRF4:397:RFX5|IRF4",   "MAF|IRF4:1819:MAF",
                           "MGA|IRF4:-76:MGA",     "MGA|IRF4:1986:MGA",
                           "MGA|IRF4:295:MGA",     "PAX5|IRF4:-51:PAX5",
                           "RFX5|IRF4:397:RFX5",   "ZBTB4|IRF4:1320:ZBTB4")
   checkEquals(sort(names(edgeData(g, attr="edgeType"))), expected.edgeNames)

} # test_.geneRegulatoryModelToGraph
#------------------------------------------------------------------------------------------------------------------------
test_.addGeneModelLayout <- function(g, xPos.span=1500)
{
   printf("--- test_.addGeneModelLayout")
   f <- system.file(package="TrenaViz", "extdata", "model.and.regRegions.irf4.top5.RData")
   load(f)

   targetGene <- "IRF4"
   tss <- getTranscriptsTable(tp, targetGene)$start
   g <- TrenaViz:::.geneRegulatoryModelToGraph(targetGene, tss, tbl.model, tbl.reg)

   g.lo <- TrenaViz:::.addGeneModelLayout(g, xPos.span=1500)

   xPos.range <- fivenum(as.numeric(nodeData(g.lo, attr="xPos")))
   checkEqualsNumeric(max(xPos.range) - min(xPos.range), 1500, tolerance=1)
   yPos <- as.numeric(nodeData(g.lo, attr="yPos"))
   checkEquals(min(yPos), -200)  # y location of the targetGene, high on the graph
   checkTrue(length(grep("^0$", yPos)) >= 6)   # y location of the binding sites

} # test_.addGeneModelLayout
#------------------------------------------------------------------------------------------------------------------------

# test_multiple.geneRegulatoryModelsToGraph <- function(display=FALSE)
# {
#    printf("--- test_multiple.geneRegulatoryModelToGraph")
#    load(system.file(package="TReNA", "extdata", "twoAQP4modelsForTesting.RData"))
#    tViz <- TrenaViz()
#
#    models <- list(wt=list(tbl.model=x.wt$tbl.model, tbl.regulatoryRegions=x.wt$tbl.regulatoryRegions),
#                   rs3875089=list(tbl.model=x.mut$tbl.model, tbl.regulatoryRegions=x.mut$tbl.regulatoryRegions))
#    g <- buildMultiModelGraph(tViz, "AQP4", models)
#    checkEquals(length(nodes(g)), 34)
#    checkEquals(length(edgeNames(g)), 46)
#
#    noa.names <- sort(names(nodeDataDefaults(g)))
#    checkEquals(length(noa.names), 33)
#    checkEquals(length(grep("rs3875089.", noa.names, fixed=TRUE)), 11)
#    checkEquals(length(grep("wt.", noa.names, fixed=TRUE)), 11)
#    g.lo <- addGeneModelLayout(tViz, g)
#
#    if(display){
#       addGraph(tViz, g.lo, names(models))
#       loadStyle(tViz, system.file(package="TrenaHelpers", "extdata", "style.js"))
#       Sys.sleep(3); fit(tViz)
#       browser();
#       xyz <- 99
#       }
#
#    return(TRUE)
#
#
# } # test_multiple.geneRegulatoryModelToGraph
#------------------------------------------------------------------------------------------------------------------------