diff --git a/DESCRIPTION b/DESCRIPTION index 789ad00..d551e30 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,5 +1,5 @@ Package: cytomapper -Version: 1.15.2 +Version: 1.15.3 Title: Visualization of highly multiplexed imaging data in R Description: Highly multiplexed imaging acquires the single-cell expression of @@ -67,5 +67,5 @@ biocViews: ImmunoOncology, Software, SingleCell, OneChannel, TwoChannel, Multipl VignetteBuilder: knitr URL: https://github.com/BodenmillerGroup/cytomapper BugReports: https://github.com/BodenmillerGroup/cytomapper/issues -RoxygenNote: 7.2.3 +RoxygenNote: 7.3.1 Encoding: UTF-8 diff --git a/NEWS b/NEWS index d65f241..c31bda4 100644 --- a/NEWS +++ b/NEWS @@ -192,3 +192,6 @@ Changes in version 1.15.1 (2023-12-10): Changes in version 1.15.2 (2023-12-13): + change of package maintenance to Lasse Meyer + +Changes in version 1.15.3 (2024-03-13): ++ measureObject fixes for Bioc 3.19 release diff --git a/R/measureObjects.R b/R/measureObjects.R index 903e862..d0b57a5 100644 --- a/R/measureObjects.R +++ b/R/measureObjects.R @@ -78,13 +78,13 @@ #' haralick (\code{h.}) features. Default features are the following: #' #' \itemize{ -#' \item{s.area}{object size in pixels} -#' \item{s.radius.mean}{mean object radius in pixels} -#' \item{m.cx}{x centroid position of object} -#' \item{m.cy}{y centroid position of object} -#' \item{m.majoraxis}{major axis length in pixels of elliptical fit} -#' \item{m.eccentricity}{elliptical eccentricity. 1 meaning straight line and 0 -#' meaning circle.} +#' \item s.area - object size in pixels +#' \item s.radius.mean - mean object radius in pixels +#' \item m.cx - x centroid position of object +#' \item m.cy - y centroid position of object +#' \item m.majoraxis - major axis length in pixels of elliptical fit +#' \item m.eccentricity - elliptical eccentricity. 1 meaning straight line and 0 +#' meaning circle. #' } #' #' @section Computing quantiles: @@ -254,8 +254,8 @@ measureObjects <- function(mask, cur_colData <- colData(object) cur_df <- cbind(mcols(image), mcols(mask)) cur_df <- cur_df[,unique(names(cur_df)), drop=FALSE] - cur_colData <- merge(as.data.frame(cur_colData), - as.data.frame(cur_df), + cur_colData <- merge(as.data.frame(as.matrix(cur_colData)), + as.data.frame(as.matrix(cur_df)), by = img_id, sort = FALSE) colData(object) <- as(cur_colData, "DataFrame") diff --git a/README.md b/README.md index 3a4824b..7d12a7b 100644 --- a/README.md +++ b/README.md @@ -143,6 +143,9 @@ Nils Eling, Nicolas Damond, Tobias Hoch, Bernd Bodenmiller (2020). cytomapper: a [Tobias Hoch](https://github.com/toobiwankenobi) +## Maintainer + +[Lasse Meyer](https://github.com/lassedochreden) ## References diff --git a/man/measureObjects.Rd b/man/measureObjects.Rd index ca66ac4..a5259fb 100644 --- a/man/measureObjects.Rd +++ b/man/measureObjects.Rd @@ -114,13 +114,13 @@ whether these features correspond to shape (\code{s.}), moment (\code{m.}) or haralick (\code{h.}) features. Default features are the following: \itemize{ -\item{s.area}{object size in pixels} -\item{s.radius.mean}{mean object radius in pixels} -\item{m.cx}{x centroid position of object} -\item{m.cy}{y centroid position of object} -\item{m.majoraxis}{major axis length in pixels of elliptical fit} -\item{m.eccentricity}{elliptical eccentricity. 1 meaning straight line and 0 -meaning circle.} +\item s.area - object size in pixels +\item s.radius.mean - mean object radius in pixels +\item m.cx - x centroid position of object +\item m.cy - y centroid position of object +\item m.majoraxis - major axis length in pixels of elliptical fit +\item m.eccentricity - elliptical eccentricity. 1 meaning straight line and 0 +meaning circle. } }