Command line or api-like automation?

[xguse]

Hello and THANK YOU for gluing these tools together!

I was wondering whether there exists a way to automate the tool? I know that I can put my own pipeline together that use these tools, but that would be kind of a waste seeing as that is basically what you have here. I was just wondering if one could or has implemented a way besides filling in a web form every time to configure and submit files to clustvis. I hope that I haven't just missed this in your documentation.

Thanks again!

[taunometsalu]

Thanks, good idea! There is no official API at the moment, but you can check the source file global.R and try to run the functions plotPCA and plotHeatmap separately. The variable data$inputSaved contains all parameters that are given to the functions.

[taunometsalu]

Just to let you know that I am in the process of refactoring the code, it is not yet made into a package (no documentation yet etc.), but you can try it out and let me know if you have any comments. You can use something like this to generate the plots:

source("https://raw.githubusercontent.com/taunometsalu/ClustVis/master/global_package.R")
d = importData("~/Downloads/0_myfile.csv")
proc = processData(d)

#pca:
pca = generatePCA(proc)
savePCA(pca, file = "~/Downloads/0_pca.pdf")

#hm:
hm = generateHeatmap(proc)
saveHeatmap(hm, file = "~/Downloads/0_hm.pdf")

[taunometsalu]

The code is now built into a proper R package, see title page of this repo for details.