PlotGeneNetworks | R Documentation |
Plots a heatmap with the distances per cluster
PlotGeneNetworks(Object, labels = F, RRmin = 10)
Object |
a pathway object |
labels |
Boolean show labels or not, or a vector with labels to be shown |
RRmin |
filter for different RR cutoff for what is an edge |
plot
IPA.files <- c(system.file("extdata", "MM10.IPA.KO.uGvsMac.Canonical_pathways.xls",package = "GeneSetCluster"), system.file("extdata", "MM10.IPA.WT.uGvsMac.Canonical_pathways.xls",package = "GeneSetCluster"), system.file("extdata", "MM10.IPA.KO.uGvsMac.Functional_annotations.xls",package = "GeneSetCluster"), system.file("extdata", "MM10.IPA.WT.uGvsMac.Functional_annotations.xls",package = "GeneSetCluster")) canonical.files <- IPA.files[grep("Canonical", IPA.files)] IPA.object1 <- LoadGeneSets(file_location = canonical.files, #where are the files groupnames= c("KO", "WT"), P.cutoff = 1.3, Mol.cutoff = 5, Source = "IPA", type = "Canonical_Pathways", structure = "SYMBOL", seperator = ",") IPA.object2 <- CombineGeneSets(Object = IPA.object1) IPA.object3 <- ClusterGeneSets(Object = IPA.object2, clusters = 7, method = "kmeans") PlotGeneNetworks(Object = IPA.object3, labels=F, RRmin = 0)
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