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broadinstitute / profiling-resistance-mechanisms

Predicting pharmacodynamic responses to cancer drugs using cell morphology
BSD 3-Clause "New" or "Revised" License
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Efforts in installing R package of ComplexHeatmap #115

Closed yhan8 closed 3 years ago

yhan8 commented 3 years ago

Script 3.resistance/signature/7.profile-heatmaps.ipynb requires an R package of ComplexHeatmap which requires the package of Cairo. https://anaconda.org/conda-forge/r-cairo. Cairo seems like an O.S. package (I am not sure though). I installed the Cairo package in brew but still cannot implement the package ComplexHeatmap successfully.

gwaybio commented 3 years ago

We will need to figure this out, since we'll likely want to generate heatmaps for the signature features at some point in the future: https://github.com/broadinstitute/profiling-resistance-mechanisms/blob/c6953675e0381dc8d4e1285908b63735c570fad3/3.resistance-signature/7.profile-heatmaps.ipynb

yhan8 commented 3 years ago

@shntnu @gwaygenomics I am following up on this

gwaybio commented 3 years ago

sorry to say @yhan8 - but these kinds of things are your responsibility to figure out :)

Part of being a data scientist is troubleshooting package installations. It might take some frustration (believe me, I have spent whole DAYS trying to install a package), but once you persevere through, the next time will be easier (less frustration).

Feel free to use this issue to document any roadblocks you encounter in the process.

yhan8 commented 3 years ago

sorry to say @yhan8 - but these kinds of things are your responsibility to figure out :)

Part of being a data scientist is troubleshooting package installations. It might take some frustration (believe me, I have spent whole DAYS trying to install a package), but once you persevere through, the next time will be easier (less frustration).

Feel free to use this issue to document any roadblocks you encounter in the process.

No worries @gwaygenomics! Just thought that you already installed this successfully on your end and Shantanu is more familiar with R, maybe you two would have a shortcut idea on where to go with this :) I'll do some digging and follow up on this later.

yhan8 commented 3 years ago

Turns out the way to make this package work is to remove the @a387b860186be1d09249128be1ff46d13101e45d

The correct code to install this package is as below: if (!("ComplexHeatmap" %in% rownames(installed.packages()))) { install_github("jokergoo/ComplexHeatmap") } suppressPackageStartupMessages(library(ComplexHeatmap))

gwaybio commented 3 years ago

Great! Glad it was that simple!