From ed4863d18003ddf639eabf374f476007301e3b5a Mon Sep 17 00:00:00 2001
From: Zizhen Yao <zizheny@alleninstitute.org>
Date: Fri, 3 Sep 2021 11:07:59 -0700
Subject: [PATCH] Add RcppParallel dependency

---
 DESCRIPTION   | 4 ++--
 R/harmonize.R | 1 +
 R/util.R      | 1 +
 3 files changed, 4 insertions(+), 2 deletions(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index 7ce3b73..568db5f 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: scrattch.hicat
 Title: Hierarchical Iterative Clustering Analysis for Transcriptomic data
-Version: 1.0.7
+Version: 1.0.8
 Authors@R: c(person("Zizhen", "Yao", email = "zizheny@alleninstitute.org", role = c("aut")),
   person("Lucas", "Graybuck", email = "lucasg@alleninstitute.org", role = c("aut", "cre")),
   person("Cindy", "van Velthoven", email = "cindy.vanvelthoven@alleninstitute.org", role = c("aut")),
@@ -18,7 +18,7 @@ Encoding: UTF-8
 LazyData: TRUE
 VignetteBuilder: knitr
 RoxygenNote: 7.0.2
-Requires: Matrix,Rphenograph,
+Requires: Matrix,Rphenograph,RcppParallel
 Imports: 
   Rcpp,
   BiocNeighbors,	
diff --git a/R/harmonize.R b/R/harmonize.R
index c754308..d9fd16a 100644
--- a/R/harmonize.R
+++ b/R/harmonize.R
@@ -24,6 +24,7 @@ prepare_harmonize<- function(dat.list, meta.df=NULL, cl.list=NULL, cl.df.list =
       dat = dat.list[[p]]
       setNames(rep(p, ncol(dat)), colnames(dat))
     }))
+    platform = factor(platform, names(dat.list))
     gene.counts <- do.call("c",lapply(names(dat.list), function(p){
       dat = dat.list[[p]]
       setNames(Matrix::colSums(dat > 0), colnames(dat))
diff --git a/R/util.R b/R/util.R
index e06f4d4..fd09ab1 100644
--- a/R/util.R
+++ b/R/util.R
@@ -714,6 +714,7 @@ get_cl_stats <- function(mat,
   if(!is.factor(cl)){
     cl = as.factor(cl)
   }
+  library(RcppParallel)
   mc.cores = mc.cores
   setThreadOptions(numThreads = mc.cores)
   transpose=FALSE