From b1683ecf135c5f20003371128484a7cc6cd13b7f Mon Sep 17 00:00:00 2001
From: Josh Cook <joshuacook0023@gmail.com>
Date: Thu, 21 Feb 2019 13:52:58 -0500
Subject: [PATCH] doc: updated for fixing scale_cosmic errors

---
 man/pal_cosmic.Rd   |  7 ++++---
 man/scale_cosmic.Rd | 14 ++------------
 2 files changed, 6 insertions(+), 15 deletions(-)

diff --git a/man/pal_cosmic.Rd b/man/pal_cosmic.Rd
index 7bfaa2e..536d193 100644
--- a/man/pal_cosmic.Rd
+++ b/man/pal_cosmic.Rd
@@ -4,7 +4,8 @@
 \alias{pal_cosmic}
 \title{COSMIC Color Palettes}
 \usage{
-pal_cosmic(palette = c("hallmarks"), alpha = 1)
+pal_cosmic(palette = c("hallmarks", "signature_substitutions"),
+  alpha = 1)
 }
 \arguments{
 \item{palette}{Palette type.
@@ -21,8 +22,8 @@ Somatic Mutations in Cancers (COSMIC)}
 }
 \examples{
 library("scales")
-show_col(pal_cosmic("hallmark")(10))
-show_col(pal_cosmic("hallmark", alpha = 0.6)(10))
+show_col(pal_cosmic("hallmarks")(10))
+show_col(pal_cosmic("hallmarks", alpha = 0.6)(10))
 show_col(pal_cosmic("signature_substitutions")(6))
 show_col(pal_cosmic("signature_substitutions", alpha = 0.6)(6))
 }
diff --git a/man/scale_cosmic.Rd b/man/scale_cosmic.Rd
index cdffb87..6cb1ef5 100644
--- a/man/scale_cosmic.Rd
+++ b/man/scale_cosmic.Rd
@@ -26,9 +26,6 @@ See \code{alpha} in \code{\link[grDevices]{rgb}} for details.}
 See \code{\link{pal_cosmic}} for details.
 }
 \examples{
-
-# TODO: change to useing this palette
-
 library("ggplot2")
 data("diamonds")
 
@@ -38,21 +35,14 @@ ggplot(
 ) +
   geom_point(alpha = 0.7) +
   geom_smooth(method = "loess", alpha = 0.1, size = 1, span = 1) +
-  theme_dark() + theme(
-    panel.background = element_rect(fill = "#2D2D2D"),
-    legend.key = element_rect(fill = "#2D2D2D")
-  ) +
-  scale_color_cosmic()
+  theme_bw() + scale_color_cosmic()
 
 ggplot(
   subset(diamonds, carat > 2.2 & depth > 55 & depth < 70),
   aes(x = depth, fill = cut)
 ) +
   geom_histogram(colour = "black", binwidth = 1, position = "dodge") +
-  theme_dark() + theme(
-    panel.background = element_rect(fill = "#2D2D2D")
-  ) +
-  scale_fill_cosmic()
+  theme_bw() + scale_fill_cosmic()
 }
 \author{
 Nan Xiao <\email{me@nanx.me}> |