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Hbiotools · Dec 22, 2021 · d851c80 · d851c80
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -27,4  27,4 @@ Suggests:
     gridExtra,
     reshape2
 Encoding: UTF-8
-RoxygenNote: 7.1.1
 RoxygenNote: 7.1.2
diff --git a/README.Rmd b/README.Rmd
@@ -18,7  18,7 @@ knitr::opts_chunk$set(
 )
 ```
 
-# ggsci <a href="https://nanx.me/ggsci/"><img src="man/figures/logo.png" align="right" height="180" /></a>
 # ggsci <img src="man/figures/logo.png" align="right" width="120" />
 
 <!-- badges: start -->
 [![R-CMD-check](https://github.com/nanxstats/ggsci/workflows/R-CMD-check/badge.svg)](https://github.com/nanxstats/ggsci/actions)

diff --git a/README.md b/README.md
@@ -1,7  1,7 @@
 
 <!-- README.md is generated from README.Rmd. Please edit that file -->
 
-# ggsci <a href="https://nanx.me/ggsci/"><img src="man/figures/logo.png" align="right" height="180" /></a>
 # ggsci <img src="man/figures/logo.png" align="right" width="120" />
 
 <!-- badges: start -->
 

diff --git a/_pkgdown.yml b/_pkgdown.yml
@@ -1,3  1,8 @@
 url: https://nanx.me/ggsci/
 
 template:
   bootstrap: 5
 
 reference:
   - title: "NPG"
     contents:

diff --git a/man/figures/README-ggsci-futurama-1.png b/man/figures/README-ggsci-futurama-1.png
diff --git a/man/figures/README-ggsci-gsea-1.png b/man/figures/README-ggsci-gsea-1.png
diff --git a/man/figures/README-ggsci-jama-1.png b/man/figures/README-ggsci-jama-1.png
diff --git a/man/figures/README-ggsci-material-1.png b/man/figures/README-ggsci-material-1.png
diff --git a/man/figures/README-ggsci-rickandmorty-1.png b/man/figures/README-ggsci-rickandmorty-1.png
diff --git a/man/figures/README-ggsci-ucscgb-1.png b/man/figures/README-ggsci-ucscgb-1.png
diff --git a/man/ggsci-package.Rd b/man/ggsci-package.Rd
diff --git a/pkgdown/extra.css b/pkgdown/extra.css
diff --git a/vignettes/ggsci.Rmd b/vignettes/ggsci.Rmd
@@ -5,15  5,22 @@ output:
     toc: true
     toc_float: true
     toc_depth: 4
-    number_sections: true
     number_sections: false
     highlight: "textmate"
     css: custom.css
 vignette: >
   %\VignetteEngine{knitr::rmarkdown}
   %\VignetteIndexEntry{Scientific Journal and Sci-Fi Themed Color Palettes for ggplot2}
 ---
 
-# Introduction
 ```{r, include=FALSE}
 knitr::opts_chunk$set(
   comment = "#>",
   collapse = TRUE
 )
 ```
 
 ## Introduction
 
 > My eyes were finally opened and I understood nature.
 >
@@ -107,7  114,7 @@ summarized in the table below.
 |                 |                              | `"blue-grey"`                  |                      |
  ----------------- ------------------------------ -------------------------------- ---------------------- 
 
-# Discrete Color Palettes
 ## Discrete Color Palettes
 
 We will use scatterplots with smooth curves, and bar plots to demonstrate
 the discrete color palettes in `ggsci`.
@@ -135,7  142,7 @@ p2 <- ggplot(
   theme_bw()
 ```
 
-## NPG
 ### NPG
 
 The NPG palette is inspired by the plots in the journals published by
 <emph>Nature Publishing Group</emph>:
@@ -146,7  153,7 @@ p2_npg <- p2   scale_fill_npg()
 grid.arrange(p1_npg, p2_npg, ncol = 2)
 ```
 
-## AAAS
 ### AAAS
 
 The AAAS palette is inspired by the plots in the journals published by
 <emph>American Association for the Advancement of Science</emph>:
@@ -157,7  164,7 @@ p2_aaas <- p2   scale_fill_aaas()
 grid.arrange(p1_aaas, p2_aaas, ncol = 2)
 ```
 
-## NEJM
 ### NEJM
 
 The NEJM palette is inspired by the plots in
 <emph>The New England Journal of Medicine</emph>:
@@ -168,7  175,7 @@ p2_nejm <- p2   scale_fill_nejm()
 grid.arrange(p1_nejm, p2_nejm, ncol = 2)
 ```
 
-## Lancet
 ### Lancet
 
 The Lancet palette is inspired by the plots in <emph>Lancet</emph> journals,
 such as <emph>Lancet Oncology</emph>:
@@ -179,7  186,7 @@ p2_lancet <- p2   scale_fill_lancet()
 grid.arrange(p1_lancet, p2_lancet, ncol = 2)
 ```
 
-## JAMA
 ### JAMA
 
 The JAMA palette is inspired by the plots in
 <emph>The Journal of the American Medical Association</emph>:
@@ -190,7  197,7 @@ p2_jama <- p2   scale_fill_jama()
 grid.arrange(p1_jama, p2_jama, ncol = 2)
 ```
 
-## JCO
 ### JCO
 
 The JCO palette is inspired by the the plots in
 <emph>Journal of Clinical Oncology</emph>:
@@ -201,7  208,7 @@ p2_jco <- p2   scale_fill_jco()
 grid.arrange(p1_jco, p2_jco, ncol = 2)
 ```
 
-## UCSCGB
 ### UCSCGB
 
 The UCSCGB palette is from the colors used by
 [UCSC Genome Browser](https://genome.ucsc.edu) for
@@ -214,7  221,7 @@ p2_ucscgb <- p2   scale_fill_ucscgb()
 grid.arrange(p1_ucscgb, p2_ucscgb, ncol = 2)
 ```
 
-## D3
 ### D3
 
 The D3 palette is from the categorical colors used by
 [D3.js](https://d3js.org) (version 3.x and before).
@@ -227,7  234,7 @@ p2_d3 <- p2   scale_fill_d3()
 grid.arrange(p1_d3, p2_d3, ncol = 2)
 ```
 
-## LocusZoom
 ### LocusZoom
 
 The LocusZoom palette is based on the colors used by
 [LocusZoom](http://locuszoom.org/).
@@ -238,7  245,7 @@ p2_locuszoom <- p2   scale_fill_locuszoom()
 grid.arrange(p1_locuszoom, p2_locuszoom, ncol = 2)
 ```
 
-## IGV
 ### IGV
 
 The IGV palette is from the colors used by
 [Integrative Genomics Viewer](http://software.broadinstitute.org/software/igv/)
@@ -251,7  258,7 @@ p2_igv_default <- p2   scale_fill_igv()
 grid.arrange(p1_igv_default, p2_igv_default, ncol = 2)
 ```
 
-## COSMIC
 ### COSMIC
 
 Color palettes inspired by the colors used in projects from the [Catalogue Of Somatic Mutations in Cancers (COSMIC)](https://cancer.sanger.ac.uk/cosmic).
 
@@ -273,7  280,7 @@ p2_cosmic_signature <- p2   scale_fill_cosmic("signature_substitutions")
 grid.arrange(p1_cosmic_signature, p2_cosmic_signature, ncol = 2)
 ```
 
-## UChicago
 ### UChicago
 
 The UChicago palette is based on
 [the colors](https://news.uchicago.edu/sites/default/files/attachments/_uchicago.identity.guidelines.pdf)
@@ -286,7  293,7 @@ p2_uchicago <- p2   scale_fill_uchicago()
 grid.arrange(p1_uchicago, p2_uchicago, ncol = 2)
 ```
 
-## Star Trek
 ### Star Trek
 
 This palette is inspired by the (uniform) colors in <emph>Star Trek</emph>:
 
@@ -296,7  303,7 @@ p2_startrek <- p2   scale_fill_startrek()
 grid.arrange(p1_startrek, p2_startrek, ncol = 2)
 ```
 
-## Tron Legacy
 ### Tron Legacy
 
 This palette is inspired by the colors used in <emph>Tron Legacy</emph>.
 It is suitable for displaying data when using a dark theme:
@@ -314,7  321,7 @@ p2_tron <- p2   theme_dark()   theme(
 grid.arrange(p1_tron, p2_tron, ncol = 2)
 ```
 
-## Futurama
 ### Futurama
 
 This palette is inspired by the colors used in the TV show <emph>Futurama</emph>:
 
@@ -324,7  331,7 @@ p2_futurama <- p2   scale_fill_futurama()
 grid.arrange(p1_futurama, p2_futurama, ncol = 2)
 ```
 
-## Rick and Morty
 ### Rick and Morty
 
 This palette is inspired by the colors used in the TV show <emph>Rick and Morty</emph>:
 
@@ -334,7  341,7 @@ p2_rickandmorty <- p2   scale_fill_rickandmorty()
 grid.arrange(p1_rickandmorty, p2_rickandmorty, ncol = 2)
 ```
 
-## The Simpsons
 ### The Simpsons
 
 This palette is inspired by the colors used in the TV show
 <emph>The Simpsons</emph>:
@@ -345,7  352,7 @@ p2_simpsons <- p2   scale_fill_simpsons()
 grid.arrange(p1_simpsons, p2_simpsons, ncol = 2)
 ```
 
-# Continuous Color Palettes
 ## Continuous Color Palettes
 
 We will use a correlation matrix visualization (a special type of heatmap)
 to demonstrate the continuous color palettes in `ggsci`.
@@ -369,7  376,7 @@ p3 <- ggplot(
   )
 ```
 
-## GSEA
 ### GSEA
 
 The GSEA palette (continuous) is inspired by the heatmaps generated by
 [GSEA GenePattern](https://software.broadinstitute.org/cancer/software/genepattern/).
@@ -380,7  387,7 @@ p3_gsea_inv <- p3   scale_fill_gsea(reverse = TRUE)
 grid.arrange(p3_gsea, p3_gsea_inv, ncol = 2)
 ```
 
-## Material Design
 ### Material Design
 
 The <emph>Material Design</emph> color palettes are from the [material design
 color guidelines](https://material.io/guidelines/style/color.html).
@@ -433,7  440,7 @@ was visualized by all plots, some palettes are more preferrable
 than the others because our eyes are more sensitive to the changes
 of their saturation levels.
 
-# Non-ggplot2 Graphics
 ## Non-ggplot2 Graphics
 
 To apply the color palettes in `ggsci` to other graphics systems
 (such as base graphics and lattice graphics), simply use the
@@ -452,7  459,7 @@ graphics systems accordingly. The transparent level of the
 entire palette is easily adjustable via the argument `"alpha"`
 in every generator or scale function.
 
-# Discussion
 ## Discussion
 
 Please note some of the palettes might not be the best choice for certain
 purposes, such as color-blind safe, photocopy safe, or print friendly.