From 1216dd2068b0badf6824a628dab9352569810755 Mon Sep 17 00:00:00 2001
From: George Chen <72078254+jiajic@users.noreply.github.com>
Date: Fri, 4 Oct 2024 09:49:24 -0400
Subject: [PATCH] chore: update naming to avoid overlapping

---
 NAMESPACE                               |  2 +-
 R/gg_settings.R                         |  8 ++++----
 R/plot_dotplot.R                        |  7 ++++---
 man/dotPlot.Rd                          |  3 ++-
 man/{theme_dark.Rd => ggplot_themes.Rd} | 11 ++++++-----
 5 files changed, 17 insertions(+), 14 deletions(-)
 rename man/{theme_dark.Rd => ggplot_themes.Rd} (57%)

diff --git a/NAMESPACE b/NAMESPACE
index ce3ea9a..1a87f04 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -93,7 +93,7 @@ export(spatPlot)
 export(spatPlot2D)
 export(spatPlot3D)
 export(subsetSankeySet)
-export(theme_dark)
+export(theme_dark2)
 export(violinPlot)
 exportClasses(giottoSankeyPlan)
 exportMethods("+")
diff --git a/R/gg_settings.R b/R/gg_settings.R
index d1d2573..20eba2d 100644
--- a/R/gg_settings.R
+++ b/R/gg_settings.R
@@ -31,12 +31,12 @@
 }
 
 
-#' @name theme_dark
-#' @title Dark plotting theme
+#' @name ggplot_themes
+#' @title ggplot2 plotting themes
 #' @description
-#' A default dark theme. It can be applied through the `theme_param`
+#' ggplot2 themes. It can be applied through the `theme_param` arg.
 #' @export
-theme_dark <- theme(
+theme_dark2 <- theme(
     plot.background = element_rect(fill = "black"),
     panel.background = element_rect(fill = "black"),
     panel.grid.major = element_blank(),
diff --git a/R/plot_dotplot.R b/R/plot_dotplot.R
index 61eacc4..147d0e3 100644
--- a/R/plot_dotplot.R
+++ b/R/plot_dotplot.R
@@ -51,7 +51,8 @@
 #'     cluster_column = "leiden_clus",
 #'     feats = feats,
 #'     dot_size = mean,
-#'     dot_color = var
+#'     dot_color = var,
+#'     dot_color_gradient = c("#EEEEFF", "#333377")
 #' )
 #' @export
 dotPlot <- function(
@@ -301,8 +302,8 @@ dotPlot <- function(
         axis_title = axis_title,
         axis_text = axis_text,
         background_color = background_color,
-        axis.ticks = element_blank(),
-        axis_text_y_angle = 0
+        axis_text_y_angle = 0,
+        axis.ticks = element_blank()
     )
     pl <- pl + do.call(.gg_theme, args = gg_theme_args)
 
diff --git a/man/dotPlot.Rd b/man/dotPlot.Rd
index 2965ad0..088e965 100644
--- a/man/dotPlot.Rd
+++ b/man/dotPlot.Rd
@@ -145,6 +145,7 @@ dotPlot(g,
     cluster_column = "leiden_clus",
     feats = feats,
     dot_size = mean,
-    dot_color = var
+    dot_color = var,
+    dot_color_gradient = c("#EEEEFF", "#333377")
 )
 }
diff --git a/man/theme_dark.Rd b/man/ggplot_themes.Rd
similarity index 57%
rename from man/theme_dark.Rd
rename to man/ggplot_themes.Rd
index f1cb534..bcd80bc 100644
--- a/man/theme_dark.Rd
+++ b/man/ggplot_themes.Rd
@@ -1,16 +1,17 @@
 % Generated by roxygen2: do not edit by hand
 % Please edit documentation in R/gg_settings.R
 \docType{data}
-\name{theme_dark}
-\alias{theme_dark}
-\title{Dark plotting theme}
+\name{ggplot_themes}
+\alias{ggplot_themes}
+\alias{theme_dark2}
+\title{ggplot2 plotting themes}
 \format{
 An object of class \code{theme} (inherits from \code{gg}) of length 10.
 }
 \usage{
-theme_dark
+theme_dark2
 }
 \description{
-A default dark theme. It can be applied through the \code{theme_param}
+ggplot2 themes. It can be applied through the \code{theme_param} arg.
 }
 \keyword{datasets}