Commit 733052fb authored by Jun Zhao's avatar Jun Zhao
Browse files

fix documentation

parent d0c494f1

NAMESPACE

+1 −1
Original line number Diff line number Diff line
@@ -7,8 +7,8 @@ export(plotCellScore) 
export(runSTG)

export(updateDAcells)

import(RANN)

import(cowplot)

import(ggplot2)

import(cowplot)

import(reticulate)

import(scales)

import(tclust)

R/STGmarkerFinder.R

+6 −0
Original line number Diff line number Diff line
@@ -40,6 +40,9 @@ STGmarkerFinder <- function( 
  lambda = 1.2, n.runs = 5, return.model = F,

  python.use = "/usr/bin/python", GPU = ""

){

  if(!inherits(X, what = "matrix") & !inherits(X, what = "Matrix")){

    X <- as.matrix(X)

  }

  # set Python

  use_python(python = python.use, required = T)
@@ -162,6 +165,9 @@ runSTG <- function( 
  lambda = 1.5, n.runs = 5, return.model = F,

  python.use = "/usr/bin/python", GPU = ""

){

  if(!inherits(X, what = "matrix") & !inherits(X, what = "Matrix")){

    X <- as.matrix(X)

  }

  # set Python

  use_python(python = python.use, required = T)

  source_python(file = paste(system.file(package="DAseq"), "DA_STG.py", sep = "/"))

R/data.R

+4 −4
Original line number Diff line number Diff line
@@ -2,7 +2,7 @@ 
#'

#' A dataset containing the top 10 PCs (principal components) of the melanoma dataset

#'

#' @source \href{https://www.sciencedirect.com/science/article/pii/S0092867418313941}

#' @source \url{https://www.sciencedirect.com/science/article/pii/S0092867418313941}

#' {Sade-Feldman, Moshe, et al. (Cell. 2018)}

"X.melanoma"
@@ -11,7 +11,7 @@ 
#' A string vector with the length equal to number of cells, indicating sample labels of each cell: which

#' sample each cell comes from

#'

#' @source \href{https://www.sciencedirect.com/science/article/pii/S0092867418313941}

#' @source \url{https://www.sciencedirect.com/science/article/pii/S0092867418313941}

#' {Sade-Feldman, Moshe, et al. (Cell. 2018)}

"X.label.melanoma"
@@ -26,7 +26,7 @@ 
#'   \item{condition}{condition of the sample label, either R or NR}

#' }

#'

#' @source \href{https://www.sciencedirect.com/science/article/pii/S0092867418313941}

#' @source \url{https://www.sciencedirect.com/science/article/pii/S0092867418313941}

#' {Sade-Feldman, Moshe, et al. (Cell. 2018)}

"X.label.info"
@@ -34,7 +34,7 @@ 
#'

#' A matrix containing 2D t-SNE embedding of the melanoma dataset

#'

#' @source \href{https://www.sciencedirect.com/science/article/pii/S0092867418313941}

#' @source \url{https://www.sciencedirect.com/science/article/pii/S0092867418313941}

#' {Sade-Feldman, Moshe, et al. (Cell. 2018)}

"X.2d.melanoma"

man/X.2d.melanoma.Rd

+1 −1
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@@ -6,7 +6,7 @@ 
\title{t-SNE embedding of the melanoma dataset}

\format{An object of class \code{matrix} with 16291 rows and 2 columns.}

\source{

\href{https://www.sciencedirect.com/science/article/pii/S0092867418313941}

\url{https://www.sciencedirect.com/science/article/pii/S0092867418313941}

{Sade-Feldman, Moshe, et al. (Cell. 2018)}

}

\usage{

man/X.label.info.Rd

+1 −1
Original line number Diff line number Diff line
@@ -10,7 +10,7 @@ 
  \item{condition}{condition of the sample label, either R or NR}

}}

\source{

\href{https://www.sciencedirect.com/science/article/pii/S0092867418313941}

\url{https://www.sciencedirect.com/science/article/pii/S0092867418313941}

{Sade-Feldman, Moshe, et al. (Cell. 2018)}

}

\usage{

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