diff --git a/DESCRIPTION b/DESCRIPTION index a3e49ae..4e9e84f 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,6 +1,6 @@ Package: ezlimmaplot Title: Bioinformatics plots using limma and ggplot2, some from output of ezlimma -Version: 0.0.3.9004 +Version: 0.0.3.9005 Authors@R: c(person("Jonathan", "Dreyfuss", role = c("aut", "cre"), email = "jdreyf@bu.edu"), person("Hui", "Pan", role = "aut"), person("Grace", "Daher", role="ctb")) @@ -36,9 +36,9 @@ Suggests: License: MIT + file LICENSE Encoding: UTF-8 LazyData: true -RoxygenNote: 7.2.3 +RoxygenNote: 7.3.1 VignetteBuilder: knitr -Remotes: +Remotes: github::jdreyf/ezlimma, github::jdreyf/Hitman, github::jdreyf/DirectionalMaxPTest diff --git a/R/bubbleplot_pwys.R b/R/bubbleplot_pwys.R index 8f19d9b..45fba28 100644 --- a/R/bubbleplot_pwys.R +++ b/R/bubbleplot_pwys.R @@ -5,6 +5,7 @@ #' numerical (i.e. non-factor) data. #' #' @param name Name of file to create. Set to \code{NA} to plot to screen instead of to file; otherwise, "_bubbleplots.pdf" is appended to the name. +#' @param ntop Integer; number of top pathways to show. #' @param caption Logical; should the caption explaining the x-axis be included? #' @inheritParams dotplot_pwys #' @inheritParams ezheat diff --git a/R/dotplot_pwys.R b/R/dotplot_pwys.R index 85dbeb4..58521d9 100644 --- a/R/dotplot_pwys.R +++ b/R/dotplot_pwys.R @@ -9,7 +9,7 @@ #' @param name Name of file to create. Set to \code{NA} to plot to screen instead of to file; otherwise, "_dotplot.pdf" is appended to the name. #' @param type.sig Either "p" or "FDR"; type of significance to show. #' @param cut.sig Numeric in [0, 1]. Pathways need to have significance of type \code{type.sig < cut.sig} in a comparison to be shown on the dot plot. -#' @param ntop Integer; number of top pathways to show. +#' @param ntop Integer; number of top pathway-by-comparison statistics to select. #' @param font.size Numeric font size of pathway names e.g. 12. #' @param mixed Character string. Should mixed statistics be included, should they be the only statistics included, or should they be excluded? #' @param reorder.rows Boolean; reorder pathways by significance before selecting \code{ntop} pathways? If not, order of \code{tab} is retained. diff --git a/man/dotplot_pwys.Rd b/man/dotplot_pwys.Rd index c665628..65dfbef 100644 --- a/man/dotplot_pwys.Rd +++ b/man/dotplot_pwys.Rd @@ -33,7 +33,7 @@ These will be the comparisons shown in the plot. If \code{NULL} these are inferr \item{cut.sig}{Numeric in [0, 1]. Pathways need to have significance of type \code{type.sig < cut.sig} in a comparison to be shown on the dot plot.} -\item{ntop}{Integer; number of top pathways to show.} +\item{ntop}{Integer; number of top pathway-by-comparison statistics to select.} \item{pwys_nm_size}{The maximum number of characters for pathway names. Longer names will be truncated.}