This repository provides a small R package of example functions for simplifying the creation of Next-Generation Clustered Heat Maps (NG-CHMs) using the ISB CGC cloud pilot.
The rstudio-isb-ngchm-demo repository provides an example RStudio system extended with this package (and the NG-CHM R package).
Load the NGCHM package and create a connection to the desired NG-CHM server(s):
> library(NGCHM)
> chmCreateManagedServer('cloud','name-of-ngchm-instance','external-ip-of-ngchm-instance')
The example shows how to connect to the managed NG-CHM server created by the ngchm-system-one system in a cloud environment.
Specify the name of the google cloud project you will use and load the ISBCHM package:
> options(cloudproject='name-of-your-google-cloud-project')
> library(ISBCHM)
Obtain data for approximately 410 cancer-related genes and 545 prostate cancer samples from the ISB CGC cloud and create an NG-CHM:
> chm <- demoCHM()
Display the NG-CHM in the viewer pane of your RStudio console:
> plot(chm)
You can expand the viewer pane to a whole browser tab/window. You can also display the NG-CHM directly in a browser tab/window:
> browseURL(chmGetURL(chm))
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