Create hex sticker

DESCRIPTION

@@ -37,6 +37,7 @@ Suggests:
     covr,
     testthat (>= 3.0.0),
     badger,
+    hexSticker,
     utils
 RoxygenNote: 7.1.2
 VignetteBuilder: knitr

README.Rmd

@@ -1,17 +1,17 @@
+```{r, echo=FALSE, include=FALSE}
+pkg <- read.dcf("DESCRIPTION", fields = "Package")[1]
+description <- read.dcf("DESCRIPTION", fields = "Description")[1]
+hex_url <- paste0('https://github.com/RajLabMSSM/',pkg,'raw/master/inst/hex/',pkg,'.png')
+```
+
 ---
-title: "README"
+title: "<img src='`r hex_url`' height='300'>"
 author: "<h4>Author: <i>Brian M. Schilder</i></h4>" 
 date: "<h4>Updated: <i>`r format( Sys.Date(), '%b-%d-%Y')`</i></h4>"
 output:
   github_document
 ---
 
-```{r, echo=FALSE, include=FALSE}
-pkg <- read.dcf("DESCRIPTION", fields = "Package")[1]
-description <- read.dcf("DESCRIPTION", fields = "Description")[1]
-```
-
-
 <!-- badges: start -->
 `r badger::badge_github_version(color = "black")` 
 `r badger::badge_github_actions(action = "R-CMD-check-bioc")`
@@ -20,25 +20,26 @@ description <- read.dcf("DESCRIPTION", fields = "Description")[1]
 `r badger::badge_license()` 
 <!-- badges: end -->
 
-# echoverse: ``r pkg``
-
-## `r description`
+## `r gsub("echoverse module: ","", description)`
 
 If you use ``r pkg``, please cite: 
 
-> Brian M Schilder, Jack Humphrey, Towfique Raj, echolocatoR: an automated end-to-end statistical and functional genomic fine-mapping pipeline, Bioinformatics, 2021;, btab658, [https://doi.org/10.1093/bioinformatics/btab658](https://doi.org/10.1093/bioinformatics/btab658)
+> Brian M Schilder, Jack Humphrey, Towfique Raj (2021) 
+echolocatoR: an automated end-to-end statistical and functional genomic
+fine-mapping pipeline, *Bioinformatics*; btab658, [https://doi.org/10.1093/bioinformatics/btab658](https://doi.org/10.1093/bioinformatics/btab658)
 
+## Installation 
 
 ```R
 if(!require("remotes")) install.packages("remotes")
 
 remotes::install_github("RajLabMSSM/`r pkg`")
 library(`r pkg`)
 ```
+## Documentation 
 
-
-## [Documentation website](https://rajlabmssm.github.io/`r pkg`) 
-## [Getting started vignette](https://rajlabmssm.github.io/`r pkg`/articles/`r pkg`) 
+### [Website](https://rajlabmssm.github.io/`r pkg`) 
+### [Getting started](https://rajlabmssm.github.io/`r pkg`/articles/`r pkg`) 
 
 <hr>
 

README.md

@@ -4,7 +4,7 @@ README
 Author: <i>Brian M. Schilder</i>
 </h4>
 <h4>
-Updated: <i>Dec-02-2021</i>
+Updated: <i>Dec-03-2021</i>
 </h4>
 
 <!-- badges: start -->
@@ -24,21 +24,25 @@ GPL-3](https://img.shields.io/badge/license-GPL--3-blue.svg)](https://cran.r-pro
 
 If you use `echoverseTemplate`, please cite:
 
-> Brian M Schilder, Jack Humphrey, Towfique Raj, echolocatoR: an
+> Brian M Schilder, Jack Humphrey, Towfique Raj (2021) echolocatoR: an
 > automated end-to-end statistical and functional genomic fine-mapping
-> pipeline, Bioinformatics, 2021;, btab658,
+> pipeline, *Bioinformatics*; btab658,
 > <https://doi.org/10.1093/bioinformatics/btab658>
 
+## Installation
+
 ``` r
 if(!require("remotes")) install.packages("remotes")
 
 remotes::install_github("RajLabMSSM/echoverseTemplate")
 library(echoverseTemplate)
 ```
 
-## [Documentation website](https://rajlabmssm.github.io/echoverseTemplate)
+## Documentation
+
+### [Website](https://rajlabmssm.github.io/echoverseTemplate)
 
-## [Getting started vignette](https://rajlabmssm.github.io/echoverseTemplate/articles/echoverseTemplate)
+### [Getting started](https://rajlabmssm.github.io/echoverseTemplate/articles/echoverseTemplate)
 
 <hr>
 

inst/CITATION

@@ -1,4 +1,4 @@
-citHeader("To cite echodata in publications use:")
+citHeader("To cite this echoverse package, please use:")
 
 citEntry(
   entry    = "Article",

inst/hex/hexSticker.Rmd

@@ -0,0 +1,125 @@
+---
+title: "hexSticker"
+author: "<h4>Author: <i>Brian M. Schilder</i></h4>" 
+date: "<h4>Updated: <i>`r format( Sys.Date(), '%b-%d-%Y')`</i></h4>"
+output:
+  BiocStyle::html_document
+vignette: >
+  %\VignetteIndexEntry{hexSticker}
+  %\VignetteEngine{knitr::rmarkdown}
+  %\VignetteEncoding{UTF-8}
+---
+
+```{r, echo=FALSE, include=FALSE}
+pkg <- read.dcf("DESCRIPTION", fields = "Package")[1]
+description <- read.dcf("DESCRIPTION", fields = "Description")[1]
+```
+
+You can make awesome hex stickers for your R packages using:
+
+- [hexSticker](https://github.com/GuangchuangYu/hexSticker)  
+- [ggimage](https://github.com/GuangchuangYu/ggimage) 
+lets you render images as data points.  
+- [ggpattern](https://coolbutuseless.github.io/package/ggpattern/)
+lets you fill objects with patterns or images.
+- [magick](https://cran.r-project.org/web/packages/magick/vignettes/intro.html) 
+modify PNGs.
+
+# `r pkg`
+
+```{r setup}
+# If you're using R<4.1.1, need this version of rvcheck
+# devtools::install_version('rvcheck',version='0.1.8') 
+library(hexSticker)
+library(dplyr)
+library(ggplot2)
+library(ggimage)
+# library(ggpattern)# remotes::install_github("coolbutuseless/ggpattern")
+```
+
+## File path
+
+Create file path.
+
+```{r}
+filename <- here::here("inst/hex", paste0(pkg,".png"))
+# filename <- file.path(tempdir(), paste0(pkg,".png"))
+dir.create(dirname(filename), showWarnings = FALSE, recursive = TRUE)
+```
+
+## Bat logo
+
+Download bat logo from the 
+[*Fine_Mapping*](https://github.com/RajLabMSSM/Fine_Mapping) GitHub repo.
+
+```{r}
+tmp <- tempfile()
+#### Side view ####
+URL <- "https://github.com/RajLabMSSM/Fine_Mapping/raw/master/echolocatoR/images/bat_silhouette.png"   
+#### Front view ####
+# URL <- "https://github.com/RajLabMSSM/Fine_Mapping/raw/master/echolocatoR/images/bat_silhouette_front.png"   
+download.file(URL, tmp)
+```
+
+## Background 
+
+Create background with `ggplot2`.
+
+```{r}
+set.seed(1234)
+n_bats <- 20
+d <- data.frame(x = -rexp(n_bats, rate = 3),
+                y = rexp(n_bats, rate = 3)
+                ) %>%
+  dplyr::mutate(image = URL,
+                bsize = abs(x*y^2)) %>%
+  dplyr::arrange(dplyr::desc(x), dplyr::desc(y))
+qplot(d$x, d$y, size=d$bsize)
+
+```
+
+
+```{r}
+gg_bats <- ggplot(d, aes(x = x, y = y, color=bsize, image=image)) + 
+  geom_image(aes(size=I(bsize)), alpha=1) +
+  scale_color_gradient(low = "#194f68", high = "#56ffff") +   
+  coord_cartesian(clip = "off") +
+  labs(title = "echoverse") +  
+  theme_void() +
+  theme(plot.title = element_text(color = "#56ffff", size = 25,
+                                  hjust = .5, vjust = 5, family = "Aller_Rg"), 
+        legend.position = "none") 
+ 
+print(gg_bats)
+```
+
+## hexSticker 
+
+```{r, eval=FALSE}    
+s_size = 1
+stick <- hexSticker::sticker(
+  subplot = gg_bats, 
+  #### Package name ####
+  package = pkg, p_size=14, p_y = 1.4,
+  #### Subplot #####
+  s_x=1, s_y=.8,  s_height = s_size, s_width = s_size,
+  #### Fill & border ####
+  h_fill = "#25355c", h_color = "#41c6c8", #56ffff
+  #### Spotlight ####
+  spotlight = TRUE, l_alpha = .3, l_width = 10,
+  #### File output ####
+  filename = filename, dpi = 300)
+print(stick)
+```
+
+
+# Session Info 
+
+<details> 
+
+```{r Session Info}
+utils::sessionInfo()
+```
+
+</details>  
+