Merge branch 'master' into fov_name_parsing_fix

angelolab · Jun 1, 2022 · e2272e7 · e2272e7
2 parents d872cf4 + 02b4549
commit e2272e7
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Showing 3 changed files with 4 additions and 2 deletions.
diff --git a/Dockerfile b/Dockerfile
@@ -38,6 +38,8 @@ RUN R -e "install.packages('arrow')"
 RUN R -e "install.packages('data.table')"
 RUN R -e "install.packages('BiocManager')"
 RUN R -e "BiocManager::install('FlowSOM')"
+RUN R -e "install.packages('devtools')"
+RUN R -e "library(devtools); devtools::install_github('angelolab/FlowSOM')" # this ensures we retrieve the forked FlowSOM
 RUN R -e "BiocManager::install('ConsensusClusterPlus')"
 
 # jupyter lab

diff --git a/ark/phenotyping/create_cell_som.R b/ark/phenotyping/create_cell_som.R
@@ -76,7 +76,7 @@ clusterCountsNormSub <- as.matrix(sweep(clusterCountsNormSub, 2, clusterCountsNo
 # create the cell SOM
 print("Run the SOM training")
 somResults <- SOM(data=as.matrix(clusterCountsNormSub), xdim=xdim, ydim=ydim,
-                  rlen=numPasses, alpha=c(lr_start, lr_end))
+                  rlen=numPasses, alpha=c(lr_start, lr_end), map=FALSE)
 
 # write the weights to feather
 print("Save trained weights")

diff --git a/ark/phenotyping/create_pixel_som.R b/ark/phenotyping/create_pixel_som.R
@@ -73,7 +73,7 @@ pixelSubsetData <- pixelSubsetData[,Map(`/`,.SD,normVals)]
 # run the SOM training step
 print("Training the SOM")
 somResults <- SOM(data=as.matrix(pixelSubsetData), rlen=numPasses,
-                  xdim=xdim, ydim=ydim, alpha=c(lr_start, lr_end))
+                  xdim=xdim, ydim=ydim, alpha=c(lr_start, lr_end), map=FALSE)
 
 # write the weights to feather
 print("Save trained weights")