Hi, I'm trying to add a heatmap with custom data to a epivizr session (as seen in the example video tutorial). From the documentation, it is not clear to me a) in which type of object the data has to be represented and b) how I can create the heatmap from within R. Does anyone have a hint? Best wishes Julian

Hi Julian, This is still a little klunky and we're working our way on making this easier in general. I've added a convenience function to do this available now on github, available on release and devel tomorrow (release:v1.2.9 and debug:v.1.3.9). See below for details. Cheers, Hector --- # example library(epivizr) data(tcga_colon_expression) ref_sample <- 2 ^ rowMeans(log2(assay(colonSE) + 1)) scaled <- (assay(colonSE) + 1) / ref_sample scaleFactor <- Biobase::rowMedians(t(scaled)) assay_normalized <- sweep(assay(colonSE), 2, scaleFactor, "/") assay(colonSE) <- log2((assay_normalized + 1) / 1e3) mz = startEpiviz() ms = mz$addMeasurements(colonSE, "colon expression") # you can add a heatmap on the browser # "Add New Heatmap" -> "epivizMs_gene1" # remove "Heatmap" filter # select samples # on versions <1.2.9 (release) and <1.3.9 (devel) # this works ch = epivizr:::EpivizChart$new(measurements=ms$getMeasurements(), mgr=mz, type="epiviz.plugins.charts.HeatmapPlot") mz$addChart(ch) # on version >=1.2.9 (release) and >= 1.3.9 (devel) ch = mz$heatmapChart(ms$getMeasurements()) On Thu, Jun 5, 2014 at 6:19 PM, Julian Gehring <julian.gehring@embl.de> wrote: > Hi, > > I'm trying to add a heatmap with custom data to a epivizr session (as seen > in the example video tutorial). From the documentation, it is not clear to > me a) in which type of object the data has to be represented and b) how I > can create the heatmap from within R. Does anyone have a hint? > > Best wishes > Julian > > _______________________________________________ > Bioconductor mailing list > Bioconductor@r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane. > science.biology.informatics.conductor > [[alternative HTML version deleted]]