Merge pull request #1 from jiajic/main

Catch up to main

DESCRIPTION

@@ -8,10 +8,12 @@ Authors@R: c(
 		 role = c("aut")),
 	person("Guo-Cheng", "Yuan", email = "guo-cheng.yuan@mssm.edu",
 		 role = c("aut")),
-  person("Matthew", "O'Brien", email = "mobrien2@bu.edu",
-	   role = c("aut")),
-	person("Joselyn", "Chávez", email = "joselynchavezf@gmail.com",
-	   role = c("aut"), comment = c(ORCID = "0000-0002-4974-4591"))
+    person("Matthew", "O'Brien", email = "mobrien2@bu.edu",
+	     role = c("aut")),
+	person("Joselyn C.", "Chávez-Fuentes", email = "joselynchavezf@gmail.com",
+	     role = c("aut"), comment = c(ORCID = "0000-0002-4974-4591")),
+	person("Edward", "Ruiz", email = "ecruiz@bu.edu",
+	     role = c("aut"))
 	)
 Maintainer: Ruben Dries <rubendries@gmail.com>
 Description: Expanded visualization and plotting functionality for Giotto Suite.

R/color_palettes.R

@@ -136,11 +136,11 @@ getDistinctColors <- function(n) {
     admitted_grey_colors = grey_colors[seq(1, 110, 10)]
     broad_colors = c(all_colors_no_grey, admitted_grey_colors)
 
-    # if too many colors warn about recycling
+    set.seed(1234)
+    on.exit(set.seed(Sys.time()))
+    # if too many colors requested, warn about recycling
     if(n > length(broad_colors)) {
       warning('\n not enough unique colors in R, maximum = 444 \n')
-      set.seed(1234)
-      on.exit(set.seed(Sys.time()))
       col_vector = sample(x = broad_colors, size = n, replace = TRUE)
     } else {
       col_vector = sample(x = broad_colors, size = n, replace = FALSE)

README.Rmd

@@ -13,7 +13,7 @@ knitr::opts_chunk$set(
 ```
 
 
-# GiottoVisuals <img src="man/figures/GiottoLogo.png" align="right" alt="" width="160" />
+# GiottoVisuals <img src="man/figures/logo.png" align="right" alt="" width="160" />
 
 <!-- badges: start -->
 ![Version](https://img.shields.io/github/r-package/v/drieslab/GiottoVisuals)
@@ -28,7 +28,7 @@ GiottoVisuals contains the main plotting functions of Giotto Suite
 
 ## Installation
 
-You can install the development version of GiottoVisuals like so:
+You can install GiottoVisuals like:
 
 ``` r
 library(remotes)

README.md

@@ -1,7 +1,7 @@
 
 <!-- README.md is generated from README.Rmd. Please edit that file -->
 
-# GiottoVisuals <img src="man/figures/GiottoLogo.png" align="right" alt="" width="160" />
+# GiottoVisuals <img src="man/figures/logo.png" align="right" alt="" width="160" />
 
 <!-- badges: start -->
 
@@ -20,7 +20,7 @@ GiottoVisuals contains the main plotting functions of Giotto Suite
 
 ## Installation
 
-You can install the development version of GiottoVisuals like so:
+You can install GiottoVisuals like:
 
 ``` r
 library(remotes)

_pkgdown.yml

@@ -1,7 +1,11 @@
 url: https://drieslab.github.io/GiottoVisuals/
 
 authors:
-  Joselyn Chávez:
+  Ruben Dries:
+    href: https://www.drieslab.com
+  Guo-Cheng Yuan:
+    href: https://labs.icahn.mssm.edu/yuanlab/
+  Joselyn C. Chávez-Fuentes:
     href: https://josschavezf.github.io
 
 template:
@@ -13,7 +17,7 @@ template:
     code_font: {google: "JetBrains Mono"}
 
 navbar:
-  bg: dark
+  bg: light
   structure:
     left:
     - intro