Merge pull request #23 from AllenInstitute/dev_njj

Fix dend saving with buildPatchseqTaxonomy

Dockerfile

@@ -59,13 +59,15 @@ RUN R -e 'remotes::install_github("AllenInstitute/scrattch.bigcat")'
 RUN R -e 'remotes::install_github("AllenInstitute/mfishtools")'
 
 ## scrattch-mapping install from local source
-COPY scrattch.mapping_0.17.tar.gz ./scrattch.mapping_0.17.tar.gz
-RUN R -e 'install.packages("scrattch.mapping_0.17.tar.gz", repos=NULL, type="source")'
+COPY scrattch.mapping_0.2.tar.gz ./scrattch.mapping_0.2.tar.gz
+RUN R -e 'install.packages("scrattch.mapping_0.2.tar.gz", repos=NULL, type="source")'
 
 ## Clean up
 RUN rm -rf /var/lib/apt/lists/*
 RUN rm -rf /tmp/downloaded_packages
 
 ## Strip binary installed libraries from RSPM
 ## https://github.com/rocker-org/rocker-versioned2/issues/340
-RUN strip /usr/local/lib/R/site-library/*/libs/*.so
+RUN strip /usr/local/lib/R/site-library/*/libs/*.so
+
+##

R/buildPatchseqTaxonomy.R

@@ -92,9 +92,6 @@ buildPatchseqTaxonomy = function(AIT.anndata,
   AIT.anndata$uns$QC_markers[[mode.name]] = file.path(taxonomyModeDir, "QC_markers.RData")
   ## TO BE UPDATED -- JEREMY
 
-  ## Save patch-seq taxonomy anndata
-  AIT.anndata$write_h5ad(file.path(taxonomyDir, "AI_taxonomy.h5ad"))
-
   ##################
   ## ------- Modify the dendrogram and save
   ##
@@ -113,6 +110,9 @@ buildPatchseqTaxonomy = function(AIT.anndata,
   ## Store the prunned dendrogram, in dend list under "patchseq" mode.name
   AIT.anndata$uns$dend[[mode.name]] = file.path(taxonomyModeDir,"dend.RData")
 
+  ## Save patch-seq taxonomy anndata
+  AIT.anndata$write_h5ad(file.path(taxonomyDir, "AI_taxonomy.h5ad"))
+
   ## Update markers after pruning
   dend = addDendrogramMarkers(AIT.anndata, mode=mode.name)
 

examples/build_taxonomy.md

@@ -55,5 +55,4 @@ AIT.anndata = loadTaxonomy("/allen/programs/celltypes/workgroups/rnaseqanalysis/
 
 ## Add markers to dendrogram
 addDendrogramMarkers(AIT.anndata = AIT.anndata)
-
 ```