update docs only

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 = "[email protected]"),
              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

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

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.