@@ -6,7 +6,7 @@

 \usage{

 runHarmony(

   inSCE,

-  useAssay = "logcounts",

+  useAssay = NULL,

   useReducedDim = NULL,

   batch = "batch",

   reducedDimName = "HARMONY",

@@ -24,10 +24,13 @@ runHarmony(

 \item{inSCE}{Input \linkS4class{SingleCellExperiment} object}

 \item{useAssay}{A single character indicating the name of the assay requiring

-batch correction. Default \code{"logcounts"}.}

+batch correction. Default \code{NULL}. It is recommended to use a reducedDim

+such as PCA through the `useReducedDim` parameter of this function.}

 \item{useReducedDim}{A single character indicating the name of the reducedDim

-used to be corrected. Specifying this will ignore \code{useAssay}. Default

+to be used. It is recommended to use a reducedDim instead of a full assay as 

+using an assay might cause the algorithm to not converge and throw error.

+Specifying this will ignore \code{useAssay}. Default

 \code{NULL}.}

 \item{batch}{A single character indicating a field in \code{colData} that

@@ -56,12 +56,12 @@ make soft kmeans cluster approach hard clustering. Default \code{0.1}.}

 \item{nIter}{An integer. The max number of iterations to perform. Default

 \code{10L}.}

+\item{seed}{Set seed for reproducibility. Default is \code{12345}.}

+

 \item{verbose}{Whether to print progress messages. Default \code{TRUE}.}

 \item{...}{Other arguments passed to \code{\link[harmony]{HarmonyMatrix}}.

 See details.}

-

-\item{Set}{seed for reproducibility. Default is \code{12345}.}

 }

 \value{

 The input \linkS4class{SingleCellExperiment} object with

@@ -15,6 +15,7 @@ runHarmony(

   theta = 5,

   sigma = 0.1,

   nIter = 10,

+  seed = 12345,

   verbose = TRUE,

   ...

 )

@@ -59,6 +60,8 @@ make soft kmeans cluster approach hard clustering. Default \code{0.1}.}

 \item{...}{Other arguments passed to \code{\link[harmony]{HarmonyMatrix}}.

 See details.}

+

+\item{Set}{seed for reproducibility. Default is \code{12345}.}

 }

 \value{

 The input \linkS4class{SingleCellExperiment} object with

@@ -79,9 +79,11 @@ work with only include: \code{nclust}, \code{tau}, \code{block.size},

 \examples{

 data('sceBatches', package = 'singleCellTK')

 logcounts(sceBatches) <- log1p(counts(sceBatches))

+\dontrun{

 if (require("harmony"))

     sceCorr <- runHarmony(sceBatches)

 }

+}

 \references{

 Ilya Korsunsky, et al., 2019

 }

@@ -79,7 +79,8 @@ work with only include: \code{nclust}, \code{tau}, \code{block.size},

 \examples{

 data('sceBatches', package = 'singleCellTK')

 logcounts(sceBatches) <- log1p(counts(sceBatches))

-sceCorr <- runHarmony(sceBatches)

+if (require("harmony"))

+    sceCorr <- runHarmony(sceBatches)

 }

 \references{

 Ilya Korsunsky, et al., 2019

@@ -20,7 +20,7 @@ runHarmony(

 )

 }

 \arguments{

-\item{inSCE}{Input \linkS4class{SingleCellExperiment} inherited object.}

+\item{inSCE}{Input \linkS4class{SingleCellExperiment} object}

 \item{useAssay}{A single character indicating the name of the assay requiring

 batch correction. Default \code{"logcounts"}.}

@@ -29,9 +29,9 @@ batch correction. Default \code{"logcounts"}.}

 used to be corrected. Specifying this will ignore \code{useAssay}. Default

 \code{NULL}.}

-\item{batch}{A single character indicating a field in

-\code{\link{colData}} that annotates the batches.

-Default \code{"batch"}.}

+\item{batch}{A single character indicating a field in \code{colData} that

+annotates the batches of each cell; or a vector/factor with the same length

+as the number of cells. Default \code{"batch"}.}

 \item{reducedDimName}{A single character. The name for the corrected

 low-dimensional representation. Will be saved to \code{reducedDim(inSCE)}.

@@ -78,7 +78,7 @@ work with only include: \code{nclust}, \code{tau}, \code{block.size},

 }

 \examples{

 data('sceBatches', package = 'singleCellTK')

-logcounts(sceBatches) <- log(counts(sceBatches) + 1)

+logcounts(sceBatches) <- log1p(counts(sceBatches))

 sceCorr <- runHarmony(sceBatches)

 }

 \references{

new file mode 100644

@@ -0,0 +1,86 @@

+% Generated by roxygen2: do not edit by hand

+% Please edit documentation in R/runBatchCorrection.R

+\name{runHarmony}

+\alias{runHarmony}

+\title{Apply Harmony batch effect correction method to SingleCellExperiment object}

+\usage{

+runHarmony(

+  inSCE,

+  useAssay = "logcounts",

+  useReducedDim = NULL,

+  batch = "batch",

+  reducedDimName = "HARMONY",

+  nComponents = 50,

+  lambda = 0.1,

+  theta = 5,

+  sigma = 0.1,

+  nIter = 10,

+  verbose = TRUE,

+  ...

+)

+}

+\arguments{

+\item{inSCE}{Input \linkS4class{SingleCellExperiment} inherited object.}

+

+\item{useAssay}{A single character indicating the name of the assay requiring

+batch correction. Default \code{"logcounts"}.}

+

+\item{useReducedDim}{A single character indicating the name of the reducedDim

+used to be corrected. Specifying this will ignore \code{useAssay}. Default

+\code{NULL}.}

+

+\item{batch}{A single character indicating a field in

+\code{\link{colData}} that annotates the batches.

+Default \code{"batch"}.}

+

+\item{reducedDimName}{A single character. The name for the corrected

+low-dimensional representation. Will be saved to \code{reducedDim(inSCE)}.

+Default \code{"HARMONY"}.}

+

+\item{nComponents}{An integer. The number of PCs to use and generate.

+Default \code{50L}.}

+

+\item{lambda}{A Numeric scalar. Ridge regression penalty parameter. Must be

+strictly positive. Smaller values result in more aggressive correction.

+Default \code{0.1}.}

+

+\item{theta}{A Numeric scalar. Diversity clustering penalty parameter. Larger

+values of theta result in more diverse clusters. theta=0 does not encourage

+any diversity. Default \code{5}.}

+

+\item{sigma}{A Numeric scalar. Width of soft kmeans clusters. Larger values

+of sigma result in cells assigned to more clusters. Smaller values of sigma

+make soft kmeans cluster approach hard clustering. Default \code{0.1}.}

+

+\item{nIter}{An integer. The max number of iterations to perform. Default

+\code{10L}.}

+

+\item{verbose}{Whether to print progress messages. Default \code{TRUE}.}

+

+\item{...}{Other arguments passed to \code{\link[harmony]{HarmonyMatrix}}.

+See details.}

+}

+\value{

+The input \linkS4class{SingleCellExperiment} object with

+\code{reducedDim(inSCE, reducedDimName)} updated.

+}

+\description{

+Harmony is an algorithm that projects cells into a shared

+embedding in which cells group by cell type rather than dataset-specific

+conditions.

+}

+\details{

+Since some of the arguments of \code{\link[harmony]{HarmonyMatrix}}

+is controlled by this wrapper function. The additional arguments users can

+work with only include: \code{nclust}, \code{tau}, \code{block.size},

+\code{max.iter.cluster}, \code{epsilon.cluster}, \code{epsilon.harmony},

+\code{plot_convergence}, \code{reference_values} and \code{cluster_prior}.

+}

+\examples{

+data('sceBatches', package = 'singleCellTK')

+logcounts(sceBatches) <- log(counts(sceBatches) + 1)

+sceCorr <- runHarmony(sceBatches)

+}

+\references{

+Ilya Korsunsky, et al., 2019

+}

deleted file mode 100644

@@ -1,61 +0,0 @@

-% Generated by roxygen2: do not edit by hand

-% Please edit documentation in R/runBatchCorrection.R

-\name{runHarmony}

-\alias{runHarmony}

-\title{Apply Harmony batch effect correction method to SingleCellExperiment object}

-\usage{

-runHarmony(

-  inSCE,

-  useAssay = "logcounts",

-  pcInput = FALSE,

-  batch = "batch",

-  reducedDimName = "HARMONY",

-  nComponents = 50L,

-  theta = 5,

-  nIter = 10L

-)

-}

-\arguments{

-\item{inSCE}{\linkS4class{SingleCellExperiment} inherited object. Required.}

-

-\item{useAssay}{A single character indicating the name of the assay requiring

-batch correction. Default \code{"logcounts"}.}

-

-\item{pcInput}{A logical scalar. Whether to use a low-dimension matrix for

-batch effect correction. If \code{TRUE}, \code{useAssay} will be searched

-from \code{reducedDimNames(inSCE)}. Default \code{FALSE}.}

-

-\item{batch}{A single character indicating a field in

-\code{\link[SummarizedExperiment]{colData}} that annotates the batches.

-Default \code{"batch"}.}

-

-\item{reducedDimName}{A single character. The name for the corrected

-low-dimensional representation. Will be saved to \code{reducedDim(inSCE)}.

-Default \code{"HARMONY"}.}

-

-\item{nComponents}{An integer. The number of principle components or

-dimensionality to generate in the resulting matrix. If \code{pcInput} is set

-to \code{TRUE}, the output dimension will follow the low-dimension matrix,

-so this argument will be ignored. Default \code{50L}.}

-

-\item{theta}{A Numeric scalar. Diversity clustering penalty parameter,

-Larger value results in more diverse clusters. Default \code{5}}

-

-\item{nIter}{An integer. The max number of iterations to perform. Default

-\code{10L}.}

-}

-\value{

-The input \linkS4class{SingleCellExperiment} object with

-\code{reducedDim(inSCE, reducedDimName)} updated.

-}

-\description{

-Harmony is an algorithm that projects cells into a shared embedding in which

-cells group by cell type rather than dataset-specific conditions.

-}

-\examples{

-data('sceBatches', package = 'singleCellTK')

-sceCorr <- runHarmony(sceBatches, nComponents = 10L)

-}

-\references{

-Ilya Korsunsky, et al., 2019

-}

@@ -1,5 +1,5 @@

 % Generated by roxygen2: do not edit by hand

-% Please edit documentation in R/runHarmony.R

+% Please edit documentation in R/runBatchCorrection.R

 \name{runHarmony}

 \alias{runHarmony}

 \title{Apply Harmony batch effect correction method to SingleCellExperiment object}

@@ -6,9 +6,9 @@

 \usage{

 runHarmony(

   inSCE,

-  exprs = "logcounts",

+  useAssay = "logcounts",

   pcInput = FALSE,

-  batchKey = "batch",

+  batch = "batch",

   reducedDimName = "HARMONY",

   nComponents = 50,

   theta = 5,

@@ -19,14 +19,14 @@ runHarmony(

 \item{inSCE}{SingleCellExperiment object. An object that stores your dataset

 and analysis procedures.}

-\item{exprs}{character, default `"logcounts"`. A string indicating the name 

+\item{useAssay}{character, default `"logcounts"`. A string indicating the name 

 of the assay requiring batch correction in "inSCE", should exist in 

 `assayNames(inSCE)`.}

 \item{pcInput}{bool, default `FALSE`. Whether to do correction on a low-dim

-matrix. If `TRUE`, will look for `exprs` in `reducedDim(inSCE)`.}

+matrix. If `TRUE`, will look for `useAssay` in `reducedDim(inSCE)`.}

-\item{batchKey}{character, default `"batch"`. A string indicating the 

+\item{batch}{character, default `"batch"`. A string indicating the 

 field of `colData(inSCE)` that defines different batches.}

 \item{reducedDimName}{character, default `"HARMONY"`. The name for the 

@@ -52,17 +52,6 @@ cells group by cell type rather than dataset-specific conditions.

 \examples{

 data('sceBatches', package = 'singleCellTK')

-sceBatches

-## class: SingleCellExperiment 

-## dim: 27610 1820 

-## metadata(0):

-## assays(3): normcounts logcounts

-## rownames(27610): GCG MALAT1 ... LOC102724004 LOC102724238

-## rowData names(0):

-## colnames(1820): reads.12732 reads.12733 ... Sample_1598 Sample_1600

-## colData names(2): cell_type1 batch

-## reducedDimNames(5): PCA

-## spikeNames(0):

 sceCorr <- runHarmony(sceBatches, nComponents = 10)

 }

 \references{

@@ -4,9 +4,16 @@

 \alias{runHarmony}

 \title{Apply Harmony batch effect correction method to SingleCellExperiment object}

 \usage{

-runHarmony(inSCE, exprs = "logcounts", pcInput = FALSE,

-  batchKey = "batch", reducedDimName = "HARMONY", nComponents = 50,

-  theta = 5, nIter = 10)

+runHarmony(

+  inSCE,

+  exprs = "logcounts",

+  pcInput = FALSE,

+  batchKey = "batch",

+  reducedDimName = "HARMONY",

+  nComponents = 50,

+  theta = 5,

+  nIter = 10

+)

 }

 \arguments{

 \item{inSCE}{SingleCellExperiment object. An object that stores your dataset

new file mode 100644

@@ -0,0 +1,63 @@

+% Generated by roxygen2: do not edit by hand

+% Please edit documentation in R/runHarmony.R

+\name{runHarmony}

+\alias{runHarmony}

+\title{Apply Harmony batch effect correction method to SingleCellExperiment object}

+\usage{

+runHarmony(inSCE, exprs = "logcounts", pcInput = FALSE,

+  batchKey = "batch", reducedDimName = "HARMONY", nComponents = 50,

+  theta = 5, nIter = 10)

+}

+\arguments{

+\item{inSCE}{SingleCellExperiment object. An object that stores your dataset

+and analysis procedures.}

+

+\item{exprs}{character, default `"logcounts"`. A string indicating the name 

+of the assay requiring batch correction in "inSCE", should exist in 

+`assayNames(inSCE)`.}

+

+\item{pcInput}{bool, default `FALSE`. Whether to do correction on a low-dim

+matrix. If `TRUE`, will look for `exprs` in `reducedDim(inSCE)`.}

+

+\item{batchKey}{character, default `"batch"`. A string indicating the 

+field of `colData(inSCE)` that defines different batches.}

+

+\item{reducedDimName}{character, default `"HARMONY"`. The name for the 

+corrected low-dimensional representation.}

+

+\item{nComponents}{integer, default `20`. Number of principle components or 

+dimensionality to generate in the resulting reducedDim. If `pcInput`, will

+directly follow the dimensionality of the specified reducedDim.}

+

+\item{theta}{Numeric, default 5. Diversity clustering penalty parameter, 

+Larger value results in more diverse clusters.}

+

+\item{nIter}{integer, default `10`. The max number of iterations to perform.}

+}

+\value{

+SingleCellExperiment object with `reducedDim(inSCE, reducedDimName)` 

+updated with corrected low-dimentional representation.

+}

+\description{

+Harmony is an algorithm that projects cells into a shared embedding in which 

+cells group by cell type rather than dataset-specific conditions.

+}

+\examples{

+ 

+data('sceBatches', package = 'singleCellTK')

+sceBatches

+## class: SingleCellExperiment 

+## dim: 27610 1820 

+## metadata(0):

+## assays(3): normcounts logcounts

+## rownames(27610): GCG MALAT1 ... LOC102724004 LOC102724238

+## rowData names(0):

+## colnames(1820): reads.12732 reads.12733 ... Sample_1598 Sample_1600

+## colData names(2): cell_type1 batch

+## reducedDimNames(5): PCA

+## spikeNames(0):

+sceCorr <- runHarmony(sceBatches, nComponents = 10)

+}

+\references{

+Ilya Korsunsky, et al., 2019

+}