From d3c7228bd99b028c2c011eaa6e8df4d0e0faaa0c Mon Sep 17 00:00:00 2001 From: kew24 Date: Wed, 3 Jan 2024 16:00:19 -0500 Subject: [PATCH] fix quote typo perpetuated in 047b929 --- R/visualization.R | 10 +++++----- man/ColorDimSplit.Rd | 2 +- man/DimPlot.Rd | 2 +- man/DotPlot.Rd | 2 +- man/FeaturePlot.Rd | 2 +- man/FeatureScatter.Rd | 2 +- man/ImageDimPlot.Rd | 2 +- man/ImageFeaturePlot.Rd | 2 +- man/VlnPlot.Rd | 2 +- 9 files changed, 13 insertions(+), 13 deletions(-) diff --git a/R/visualization.R b/R/visualization.R index 04937db62..9629c9d4e 100644 --- a/R/visualization.R +++ b/R/visualization.R @@ -581,7 +581,7 @@ RidgePlot <- function( #' @param pt.size Point size for points #' @param alpha Alpha value for points #' @param split.by A factor in object metadata to split the plot by, pass 'ident' -#' to split by cell identity' +#' to split by cell identity #' @param split.plot plot each group of the split violin plots by multiple or #' single violin shapes. #' @param adjust Adjust parameter for geom_violin @@ -798,7 +798,7 @@ ColorDimSplit <- function( #' @param group.by Name of one or more metadata columns to group (color) cells by #' (for example, orig.ident); pass 'ident' to group by identity class #' @param split.by A factor in object metadata to split the plot by, pass 'ident' -#' to split by cell identity' +#' to split by cell identity #' @param shape.by If NULL, all points are circles (default). You can specify any #' cell attribute (that can be pulled with FetchData) allowing for both #' different colors and different shapes on cells. Only applicable if \code{raster = FALSE}. @@ -1015,7 +1015,7 @@ DimPlot <- function( #' @param min.cutoff,max.cutoff Vector of minimum and maximum cutoff values for each feature, #' may specify quantile in the form of 'q##' where '##' is the quantile (eg, 'q1', 'q10') #' @param split.by A factor in object metadata to split the plot by, pass 'ident' -#' to split by cell identity' +#' to split by cell identity #' @param keep.scale How to handle the color scale across multiple plots. Options are: #' \itemize{ #' \item \dQuote{feature} (default; by row/feature scaling): The plots for @@ -1970,7 +1970,7 @@ CellScatter <- function( #' @param pt.size Size of the points on the plot #' @param shape.by Ignored for now #' @param split.by A factor in object metadata to split the feature plot by, pass 'ident' -#' to split by cell identity' +#' to split by cell identity #' @param span Spline span in loess function call, if \code{NULL}, no spline added #' @param smooth Smooth the graph (similar to smoothScatter) #' @param slot Slot to pull data from, should be one of 'counts', 'data', or 'scale.data' @@ -4344,7 +4344,7 @@ BarcodeInflectionsPlot <- function(object) { #' @param idents Identity classes to include in plot (default is all) #' @param group.by Factor to group the cells by #' @param split.by A factor in object metadata to split the plot by, pass 'ident' -#' to split by cell identity' +#' to split by cell identity #' see \code{\link{FetchData}} for more details #' @param cluster.idents Whether to order identities by hierarchical clusters #' based on given features, default is FALSE diff --git a/man/ColorDimSplit.Rd b/man/ColorDimSplit.Rd index 33efebabd..bfb9202d2 100644 --- a/man/ColorDimSplit.Rd +++ b/man/ColorDimSplit.Rd @@ -38,7 +38,7 @@ See \code{\link{DiscretePalette}} for details.} \item{\code{group.by}}{Name of one or more metadata columns to group (color) cells by (for example, orig.ident); pass 'ident' to group by identity class} \item{\code{split.by}}{A factor in object metadata to split the plot by, pass 'ident' -to split by cell identity'} +to split by cell identity} \item{\code{shape.by}}{If NULL, all points are circles (default). You can specify any cell attribute (that can be pulled with FetchData) allowing for both different colors and different shapes on cells. Only applicable if \code{raster = FALSE}.} diff --git a/man/DimPlot.Rd b/man/DimPlot.Rd index a46a402f0..aa2212b94 100644 --- a/man/DimPlot.Rd +++ b/man/DimPlot.Rd @@ -63,7 +63,7 @@ See \code{\link{DiscretePalette}} for details.} (for example, orig.ident); pass 'ident' to group by identity class} \item{split.by}{A factor in object metadata to split the plot by, pass 'ident' -to split by cell identity'} +to split by cell identity} \item{shape.by}{If NULL, all points are circles (default). You can specify any cell attribute (that can be pulled with FetchData) allowing for both diff --git a/man/DotPlot.Rd b/man/DotPlot.Rd index f59e9fa2e..e00fc1947 100644 --- a/man/DotPlot.Rd +++ b/man/DotPlot.Rd @@ -54,7 +54,7 @@ gene will have no dot drawn.} \item{group.by}{Factor to group the cells by} \item{split.by}{A factor in object metadata to split the plot by, pass 'ident' - to split by cell identity' +to split by cell identity see \code{\link{FetchData}} for more details} \item{cluster.idents}{Whether to order identities by hierarchical clusters diff --git a/man/FeaturePlot.Rd b/man/FeaturePlot.Rd index fa5c4293a..6fbc593bd 100644 --- a/man/FeaturePlot.Rd +++ b/man/FeaturePlot.Rd @@ -81,7 +81,7 @@ may specify quantile in the form of 'q##' where '##' is the quantile (eg, 'q1', \item{reduction}{Which dimensionality reduction to use. If not specified, first searches for umap, then tsne, then pca} \item{split.by}{A factor in object metadata to split the plot by, pass 'ident' -to split by cell identity'} +to split by cell identity} \item{keep.scale}{How to handle the color scale across multiple plots. Options are: \itemize{ diff --git a/man/FeatureScatter.Rd b/man/FeatureScatter.Rd index 06e6625d7..8ae12c3df 100644 --- a/man/FeatureScatter.Rd +++ b/man/FeatureScatter.Rd @@ -47,7 +47,7 @@ useful for crowded plots if points of interest are being buried. (default is FAL (for example, orig.ident); pass 'ident' to group by identity class} \item{split.by}{A factor in object metadata to split the feature plot by, pass 'ident' -to split by cell identity'} +to split by cell identity} \item{cols}{Colors to use for identity class plotting.} diff --git a/man/ImageDimPlot.Rd b/man/ImageDimPlot.Rd index 3667c3ef4..8044ce694 100644 --- a/man/ImageDimPlot.Rd +++ b/man/ImageDimPlot.Rd @@ -46,7 +46,7 @@ segmentation boundaries} (for example, orig.ident); pass 'ident' to group by identity class} \item{split.by}{A factor in object metadata to split the plot by, pass 'ident' -to split by cell identity'} +to split by cell identity} \item{cols}{Vector of colors, each color corresponds to an identity class. This may also be a single character or numeric value corresponding to a palette as specified by \code{\link[RColorBrewer]{brewer.pal.info}}. diff --git a/man/ImageFeaturePlot.Rd b/man/ImageFeaturePlot.Rd index c5dbd50e5..4e5041cc6 100644 --- a/man/ImageFeaturePlot.Rd +++ b/man/ImageFeaturePlot.Rd @@ -73,7 +73,7 @@ When blend is \code{TRUE}, takes anywhere from 1-3 colors: may specify quantile in the form of 'q##' where '##' is the quantile (eg, 'q1', 'q10')} \item{split.by}{A factor in object metadata to split the plot by, pass 'ident' -to split by cell identity'} +to split by cell identity} \item{molecules}{A vector of molecules to plot} diff --git a/man/VlnPlot.Rd b/man/VlnPlot.Rd index 00be2eb10..d84009d50 100644 --- a/man/VlnPlot.Rd +++ b/man/VlnPlot.Rd @@ -53,7 +53,7 @@ expression of the attribute being potted, can also pass 'increasing' or 'decreas \item{group.by}{Group (color) cells in different ways (for example, orig.ident)} \item{split.by}{A factor in object metadata to split the plot by, pass 'ident' -to split by cell identity'} +to split by cell identity} \item{adjust}{Adjust parameter for geom_violin}