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
>
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