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d3b-center / hope-cohort-analysis

Analysis for HOPE cohort
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Annotation file for data availability plot #97

Closed komalsrathi closed 3 months ago

komalsrathi commented 4 months ago

Based on slack request from @mkoptyra the file used for data availability plot is needed by Nicole and Pei. This PR writes the respective file out.

komalsrathi commented 3 months ago

Same for this, could this be reviewed and merged if possible?

jharenza commented 3 months ago

root@XXX:/home/rstudio/hope-cohort-analysis/analyses/data-availability# Rscript --vanilla 03-clinical_data_availability_age_continuous.R Error: package or namespace load failed for ‘ComplexHeatmap’ in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]): namespace ‘circlize’ 0.4.9 is being loaded, but >= 0.4.14 is required Execution halted

It looks like we need a new version of circlize in the docker image - have you been running in the image or outside of it. I will update it when I update the docker image.

Also, should there be two 03 scripts in this module? If so, can you update the run script and README in this PR to add the second one 03-clinical_data_availability_age_continuous_cns_region.R

komalsrathi commented 3 months ago

The two scripts have the same numerical prefix because they are not sequential but rather can be run at the same time.

komalsrathi commented 3 months ago

I removed that script because it is not being used/not required for the manuscript.