tna.plot.gsea1 {RTN} | R Documentation |
This function takes a TNA object and plots the one-tailed GSEA results for individual regulons.
tna.plot.gsea1(object, labPheno="tna", file=labPheno, filepath=".", regulon.order="size", ntop=NULL, tfs=NULL, ylimPanels=c(0.0,3.5,0.0,0.8), heightPanels=c(1,1,3), width=4.4, height=4, ylabPanels=c("Phenotype","Regulon","Enrichment score"), xlab="Position in the ranked list of genes", alpha=0.5, sparsity=10, autoformat=TRUE, plotpdf=TRUE, ...)
object |
an object of class 'TNA' |
file |
a character string naming a file. |
filepath |
a single character value specifying where to store GSEA figures. |
regulon.order |
a single character value specifying whether regulons should be ordered by 'size', 'score', 'pvalue', 'adj.pvalue' and 'name' (or 'none' to keep the input ordering). |
ntop |
a single integer value specifying how many regulons of top significance will be plotted. |
tfs |
an optional vector with transcription factor identifiers (this option overrides the 'ntop' argument). |
ylimPanels |
a numeric vector of length=4 specifying y coordinates ranges of the 1st and 3th plots (i.e. ylim for 'Phenotypes' and 'Running enrichment score'). |
heightPanels |
a numeric vector of length=3 specifying the relative height of each panel in the plot. |
width |
a single numeric value specifying the width of the graphics region in inches. |
height |
a single numeric value specifying the height of the graphics region in inches. |
ylabPanels |
a character vector of length=3 specifying the the title for the y axes. |
xlab |
a single character value specifying the the title for the x axis. |
labPheno |
a single character value specifying a label for the phenotype (will also be used as the name of output file). |
alpha |
a single numeric value in [0,1] specifying the transparency of the hits in the ranked list. |
sparsity |
a single integer value (>1) specifying the density of the dots representing the running score. |
autoformat |
a single logical value specifying to set the graph format using predefined themes. This option overrides the "ylimPanels" argument. |
plotpdf |
a single logical value specifying to whether to plot a PDF file or directly to Viewer. |
... |
other arguments used by the function pdf. |
Mauro Castro
data(dt4rtn) # select 5 regulatoryElements for a quick demonstration! tfs4test <- dt4rtn$tfs[c("PTTG1","E2F2","FOXM1","E2F3","RUNX2")] ## Not run: rtni <- tni.constructor(expData=dt4rtn$gexp, regulatoryElements=tfs4test, rowAnnotation=dt4rtn$gexpIDs) rtni<-tni.permutation(rtni) rtni<-tni.bootstrap(rtni) rtni<-tni.dpi.filter(rtni) rtna<-tni2tna.preprocess(rtni, phenotype=dt4rtn$pheno, hits=dt4rtn$hits, phenoIDs=dt4rtn$phenoIDs) # run GSEA analysis pipeline rtna <- tna.gsea1(rtna, stepFilter=FALSE) # plot available GSEA results tna.plot.gsea1(rtna, labPheno="test") ## End(Not run)