Merge pull request #30 from jhsiao999/dev

Dev
jhsiao999 · Oct 29, 2019 · e0f8604 · e0f8604
2 parents 9606bb8 + f8e7a53
commit e0f8604
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Showing 29 changed files with 868 additions and 872 deletions.
diff --git a/.gitignore b/.gitignore
@@ -4,7 +4,6 @@ peco.Rcheck/
 peco*tar.gz
 vignettes/*.html
 vignettes/*.R
-NOTES.txt
 peco.Rproj
 doc
 Meta

diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,17 +1,17 @@
 Encoding: UTF-8
 Type: Package
 Package: peco
-Version: 0.99.4
+Version: 0.99.5
 Date: 2019-09-19
 Title: A Supervised Approach for **P**r**e**dicting **c**ell Cycle
     Pr**o**gression using scRNA-seq data
 Authors@R: c(
-       person("Chiaowen Joyce","Hsiao", email="joyce.hsiao1@gmail.com", 
+        person("Chiaowen Joyce","Hsiao", email="joyce.hsiao1@gmail.com", 
                     role=c("aut","cre")),
-       person("Matthew", "Stephens", email="stephens999@gmail.com", role="aut"),
-       person("John", "Blischak", email = "jdblischak@gmail.com", role="ctb"),
-       person("Peter", "Carbonetto", email = "peter.carbonetto@gmail.com",
-              role="ctb"))
+        person("Matthew", "Stephens", email="stephens999@gmail.com", role="aut"),
+        person("John", "Blischak", email = "jdblischak@gmail.com", role="ctb"),
+        person("Peter", "Carbonetto", email = "peter.carbonetto@gmail.com",
+                role="ctb"))
 Description: Our approach provides a way to assign continuous cell cycle phase 
     using scRNA-seq data, and consequently, allows to identify cyclic trend 
     of gene expression levels along the cell cycle. This package provides method
@@ -32,14 +32,16 @@ Imports:
     graphics,
     methods (>= 1.7.1),
     parallel (>= 3.5.1),
+    scater (>= 1.10.1),
     SingleCellExperiment (>= 1.4.1),
+    SummarizedExperiment (>= 1.12.0),
     stats,
     utils
 Suggests: 
     knitr,
     rmarkdown
 biocViews:
-  Sequencing, RNASeq, GeneExpression, Transcriptomics, SingleCell,
-  Software, StatisticalMethod, Classification, Visualization
+    Sequencing, RNASeq, GeneExpression, Transcriptomics, SingleCell,
+    Software, StatisticalMethod, Classification, Visualization
 VignetteBuilder: knitr
 RoxygenNote: 6.1.1
diff --git a/NAMESPACE b/NAMESPACE
@@ -12,25 +12,38 @@ export(intensity2circle)
 export(rotation)
 export(shift_origin)
 import(SingleCellExperiment)
-import(doParallel)
 import(foreach)
 import(methods)
 import(parallel)
-importFrom(assertthat,assert_that)
+importFrom(SingleCellExperiment,SingleCellExperiment)
+importFrom(SingleCellExperiment,cpm)
+importFrom(SummarizedExperiment,"assayNames<-")
+importFrom(SummarizedExperiment,"assays<-")
+importFrom(SummarizedExperiment,"colData<-")
+importFrom(SummarizedExperiment,assay)
+importFrom(SummarizedExperiment,assayNames)
+importFrom(SummarizedExperiment,assays)
+importFrom(SummarizedExperiment,colData)
+importFrom(assertthat,has_name)
 importFrom(circular,coord2rad)
 importFrom(conicfit,AtoG)
 importFrom(conicfit,EllipseDirectFit)
 importFrom(conicfit,Residuals.ellipse)
 importFrom(conicfit,calculateEllipse)
+importFrom(doParallel,registerDoParallel)
 importFrom(genlasso,cv.trendfilter)
 importFrom(genlasso,trendfilter)
 importFrom(graphics,plot)
 importFrom(graphics,points)
+importFrom(parallel,makeCluster)
+importFrom(parallel,stopCluster)
+importFrom(scater,calculateCPM)
 importFrom(stats,approxfun)
 importFrom(stats,dnorm)
 importFrom(stats,loess)
 importFrom(stats,prcomp)
 importFrom(stats,predict)
+importFrom(stats,qqnorm)
 importFrom(stats,smooth.spline)
 importFrom(stats,var)
 importFrom(utils,globalVariables)
diff --git a/NEWS b/NEWS
@@ -1,3 +1,9 @@
+Changes in version 0.99.3 (2019-09-19)
++ cycle_npreg_outsample outputs SingleCellExperiment object
++ data_transform_quantile inputs and outputs SingleCellExperiment object
++ Fixed @import and @importFrom
++ Fix BiocCheck notes
+
 Changes in version 0.99.3 (2019-09-19)
 + Changed to store data in SingleCellExperiment objects
 

diff --git a/R/circ_dist.R b/R/circ_dist.R
@@ -20,7 +20,8 @@
 #'
 #' # after rotation of angles, difference is 0 between the original
 #' # and the shifted angles
-#' theta_compare_rotated <- rotation(ref_var=theta_ref, shift_var=theta_compare)
+#' theta_compare_rotated <- rotation(ref_var=theta_ref,
+#'     shift_var=theta_compare)
 #' mean(circ_dist(theta_ref, theta_compare_rotated))
 #'
 #'
@@ -77,7 +78,7 @@ rotation <- function(ref_var,shift_var) {
     which_cutoff <- which.min(df$dis)
 
     shift_var_new <-
-      df$flip[which_cutoff]*((shift_var+df$shift[which_cutoff])%%(2*pi))
+        df$flip[which_cutoff]*((shift_var+df$shift[which_cutoff])%%(2*pi))
 
     return(shift_var_new)
 }