From 8793995e633f428f4944d022af6aa033bbc5e34c Mon Sep 17 00:00:00 2001 From: Dan Knight Date: Wed, 2 Oct 2024 14:39:11 -0700 Subject: [PATCH 1/4] Fix lattice::draw.key reference in documentation --- NEWS.md | 6 +++--- man/legend.grob.Rd | 2 +- 2 files changed, 4 insertions(+), 4 deletions(-) diff --git a/NEWS.md b/NEWS.md index c271db6..d4ac29b 100644 --- a/NEWS.md +++ b/NEWS.md @@ -2003,7 +2003,7 @@ BoutrosLab.plotting.general 5.3.7 - `create.heatmap`: Use grobPack() fontfamily specification to avoid unknown Arial font specification - `create.dotmap`: Changed yaxis label default to not be bold - Legend.grob: Added parameters - 'layout', 'between.col', 'between.row' to allow user to specify layout for multiple legends and set empty space between rows/columns -- Legend.grob: Changed titles in legend to use a text grob instead of draw.key +- Legend.grob: Changed titles in legend to use a text grob instead of `draw.key` - `create.heatmap`: Added 'legend.layout', 'legend.between.col', and 'legend.between.row' parameters # BoutrosLab.plotting.general 3.5.4 (2012-11-02) @@ -2067,7 +2067,7 @@ BoutrosLab.plotting.general 5.3.7 ## Changed - `create.heatmap`: Added code to close devices opened by the grid::covertUnit function and remove Rplots.pdf files if necessary -- Legend.grob: Added code to remove Rplots.pdf files created by the lattice::draw.key +- Legend.grob: Added code to remove Rplots.pdf files created by the lattice::`draw.key` # BoutrosLab.plotting.general 3.4.0 (2012-09-12) @@ -2088,7 +2088,7 @@ BoutrosLab.plotting.general 5.3.7 ## Changed -- Legend.grob: Added code to close extra device created by the draw.key() +- Legend.grob: Added code to close extra device created by the `draw.key`() # BoutrosLab.plotting.general 3.3.5 (2012-08-29) diff --git a/man/legend.grob.Rd b/man/legend.grob.Rd index 9235960..62ae645 100644 --- a/man/legend.grob.Rd +++ b/man/legend.grob.Rd @@ -45,7 +45,7 @@ The 'colours' component is a vector of fill colours to be used for the rectangle } \value{Returns an grob representing the legend(s)} \author{Lauren Chong} -\seealso{\code{\link{create.heatmap}}, \code{\link{draw.key}}, \code{\link{gpar}}} +\seealso{\code{\link{create.heatmap}}, \code{\link{lattice::draw.key}}, \code{\link{gpar}}} \section{Implementation}{ This function was initially created to be called from \code{create.heatmap} to draw a covariate legend.\cr The decision to use a grob (grid graphical object) to represent the legend was made based on the format of the \code{levelplot} function in the \code{lattice} package. Since the \code{legend} argument of the function requires grobs, it was easiest to create a grob to represent the legend and then, if necessary, add this to any existing grobs (dendrograms, etc.) in the \code{create.heatmap} function using a grid layout.\cr From 10cf6eb0795730d61ceb46a40627b520e5d1d8a7 Mon Sep 17 00:00:00 2001 From: Dan Knight Date: Wed, 2 Oct 2024 14:39:59 -0700 Subject: [PATCH 2/4] Fix comment length in manual --- man/create.scatterplot.Rd | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/man/create.scatterplot.Rd b/man/create.scatterplot.Rd index 87dc503..a4fde5e 100644 --- a/man/create.scatterplot.Rd +++ b/man/create.scatterplot.Rd @@ -901,7 +901,8 @@ create.scatterplot( xlab.cex = 1.5, ylab.cex = 1.5, # To plot ROC curve, add "s" or "S" to type vector. - # "s" connects points with the vertical segment first. "S" connects points with the horizontal segment first. + # "s" connects points with the vertical segment first. + # "S" connects points with the horizontal segment first. type = 's', lwd = 3, add.xyline = TRUE, From 84b1682060a70fc459eed326790873dbe3840f34 Mon Sep 17 00:00:00 2001 From: Dan Knight Date: Wed, 2 Oct 2024 14:40:58 -0700 Subject: [PATCH 3/4] Update changelog --- NEWS.md | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/NEWS.md b/NEWS.md index d4ac29b..8c8cbe0 100644 --- a/NEWS.md +++ b/NEWS.md @@ -10,7 +10,11 @@ ## Changed - Improved documentation for type parameter in `create.scatterplot` + + +## Fixed - Fix typo in README +- Update package manual for CRAN standards # BoutrosLab.plotting.general 7.1.0 (2023-10-26) From b22d7f5ebb6375cbc93c388999401860fe43768d Mon Sep 17 00:00:00 2001 From: Dan Knight Date: Wed, 2 Oct 2024 15:07:08 -0700 Subject: [PATCH 4/4] Link to lattice in manpage --- man/legend.grob.Rd | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/man/legend.grob.Rd b/man/legend.grob.Rd index 62ae645..2bdc6fd 100644 --- a/man/legend.grob.Rd +++ b/man/legend.grob.Rd @@ -45,7 +45,7 @@ The 'colours' component is a vector of fill colours to be used for the rectangle } \value{Returns an grob representing the legend(s)} \author{Lauren Chong} -\seealso{\code{\link{create.heatmap}}, \code{\link{lattice::draw.key}}, \code{\link{gpar}}} +\seealso{\code{\link{create.heatmap}}, \code{\link[lattice]{draw.key}}, \code{\link{gpar}}} \section{Implementation}{ This function was initially created to be called from \code{create.heatmap} to draw a covariate legend.\cr The decision to use a grob (grid graphical object) to represent the legend was made based on the format of the \code{levelplot} function in the \code{lattice} package. Since the \code{legend} argument of the function requires grobs, it was easiest to create a grob to represent the legend and then, if necessary, add this to any existing grobs (dendrograms, etc.) in the \code{create.heatmap} function using a grid layout.\cr