diff --git a/DESCRIPTION b/DESCRIPTION index 7d2af37..123513b 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -12,8 +12,8 @@ Authors@R: c( person("Leo", "Lahti", role=c("ctb"), email="leo.lahti@utu.fi", comment = c(ORCID = "0000-0001-5537-637X")), person("Tuomas", "Borman", role = c("ctb"), comment = c(ORCID = "0000-0002-8563-8884")) ) -Version: 1.33.1 -Date: 2024-06-04 +Version: 1.33.2 +Date: 2024-06-21 License: GPL-3 Title: Single-Cell Analysis Toolkit for Gene Expression Data in R Description: A collection of tools for doing various analyses of diff --git a/R/plotColData.R b/R/plotColData.R index c929b45..a6811f0 100644 --- a/R/plotColData.R +++ b/R/plotColData.R @@ -36,8 +36,7 @@ #' @param summary_fun Function to summarize the feature value of each point #' (e.g. gene expression of each cell) when the points binned, defaults to #' \code{sum}. Can be either the name of the function or the function itself. -#' @param hex Logical, whether to use \code{\link{geom_hex}}. Note that -#' \code{geom_hex} is broken in \code{ggplot2} version 3.4.0. +#' @param hex Logical, whether to use \code{\link{geom_hex}}. #' @param ... Additional arguments for visualization, see #' \code{?"\link{scater-plot-args}"} for details. #' diff --git a/man/plotColData.Rd b/man/plotColData.Rd index c8021a9..2e09b46 100644 --- a/man/plotColData.Rd +++ b/man/plotColData.Rd @@ -72,8 +72,7 @@ x and y are numeric.} (e.g. gene expression of each cell) when the points binned, defaults to \code{sum}. Can be either the name of the function or the function itself.} -\item{hex}{Logical, whether to use \code{\link{geom_hex}}. Note that -\code{geom_hex} is broken in \code{ggplot2} version 3.4.0.} +\item{hex}{Logical, whether to use \code{\link{geom_hex}}.} \item{by.assay.type}{A string or integer scalar specifying which assay to obtain expression values from, for use in point aesthetics - see \code{?\link{retrieveCellInfo}} for diff --git a/man/plotExpression.Rd b/man/plotExpression.Rd index cc2fac7..07c9784 100644 --- a/man/plotExpression.Rd +++ b/man/plotExpression.Rd @@ -96,8 +96,7 @@ x and y are numeric.} (e.g. gene expression of each cell) when the points binned, defaults to \code{sum}. Can be either the name of the function or the function itself.} -\item{hex}{Logical, whether to use \code{\link{geom_hex}}. Note that -\code{geom_hex} is broken in \code{ggplot2} version 3.4.0.} +\item{hex}{Logical, whether to use \code{\link{geom_hex}}.} \item{by.assay.type}{A string or integer scalar specifying which assay to obtain expression values from, for use in point aesthetics - see the \code{assay.type} argument in \code{?\link{retrieveCellInfo}}. Also the alias \code{by.assay.type} is accepted.} diff --git a/man/plotReducedDim.Rd b/man/plotReducedDim.Rd index 0c10725..5068200 100644 --- a/man/plotReducedDim.Rd +++ b/man/plotReducedDim.Rd @@ -114,8 +114,7 @@ x and y are numeric.} (e.g. gene expression of each cell) when the points binned, defaults to \code{sum}. Can be either the name of the function or the function itself.} -\item{hex}{Logical, whether to use \code{\link{geom_hex}}. Note that -\code{geom_hex} is broken in \code{ggplot2} version 3.4.0.} +\item{hex}{Logical, whether to use \code{\link{geom_hex}}.} \item{by.assay.type}{A string or integer scalar specifying which assay to obtain expression values from,