Question: epivizr: Input data type for heatmap
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gravatar for Julian Gehring
5.5 years ago by
Julian Gehring1.3k
Julian Gehring1.3k 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
epivizr • 500 views
ADD COMMENTlink modified 5.5 years ago by Hector Corrada Bravo60 • written 5.5 years ago by Julian Gehring1.3k
Answer: epivizr: Input data type for heatmap
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gravatar for Hector Corrada Bravo
5.5 years ago by
United States
Hector Corrada Bravo60 wrote:
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]]
ADD COMMENTlink written 5.5 years ago by Hector Corrada Bravo60
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