move README pictures into man/figures/

DESCRIPTION

@@ -2,8 +2,10 @@ Package: gglogo
 Title: Geom for Logo Sequence Plots
 Version: 0.1.5
 Authors@R: c(
- person("Heike", "Hofmann", email = "hofmann@iastate.edu", role = "aut"),
- person("Eric", "Hare", email = "eric@oaiti.org", role = c("aut", "cre")),
+ person("Heike", "Hofmann", email = "hofmann@iastate.edu", role = "aut",
+ comment = c(ORCID = "0000-0001-6216-5183")),
+ person("Eric", "Hare", email = "eric@oaiti.org", role = c("aut", "cre"), 
+ comment = c(ORCID = "0000-0002-4277-3146")),
  person("GGobi Foundation", role = "aut"))
 License: GPL-3
 URL: https://github.com/heike/gglogo, http://heike.github.io/gglogo/

NEWS.md

@@ -5,7 +5,18 @@
 
 ## Small Usage Changes
 
-- add parameter `missing_encode` to convert corresponding symbols in sequences correctly to `NA`
+- expanded documentation
+- add parameter `missing_encode` in `ggfortify` to convert corresponding symbols in sequences correctly to `NA`
+
+## Bug fixes
+
+
+# gglogo 0.1.4
+
+
+## Brand New Features
+
+## Small Usage Changes
 
 ## Bug fixes
 

README.Rmd

@@ -8,7 +8,7 @@ output:
 ---
 
 ```{r setup, include=FALSE}
-knitr::opts_chunk$set(echo = TRUE)
+knitr::opts_chunk$set(echo = TRUE, fig.path = "man/figures/")
 ```
 
 R package for creating sequence logo plots

README.md

@@ -14,7 +14,6 @@ R package for creating sequence logo plots
 <!-- badges: start -->
 [![CRAN Status](http://www.r-pkg.org/badges/version/gglogo)](https://cran.r-project.org/package=gglogo) [![CRAN RStudio mirror downloads](https://cranlogs.r-pkg.org/badges/last-month/gglogo?color=blue)](https://r-pkg.org/pkg/gglogo)
 [![Last-changedate](https://img.shields.io/badge/last%20change-2024--01--30-yellowgreen.svg)](https://github.com/heike/gglogo/commits/main)
-[![codecov test coverage](https://codecov.io/gh/heike/gglogo/graph/badge.svg?token=zfeqffIjxY)](https://codecov.io/gh/heike/gglogo)
 [![R-CMD-check](https://github.com/heike/gglogo/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/heike/gglogo/actions/workflows/R-CMD-check.yaml)
 [![Codecov test coverage](https://codecov.io/gh/heike/gglogo/branch/main/graph/badge.svg)](https://app.codecov.io/gh/heike/gglogo?branch=main)
 <!-- badges: end -->
@@ -77,7 +76,7 @@ ggplot(data = ggfortify(sequences, peptide, method="shannon")) +
  theme(legend.position = "bottom") 
 ```
 
-![](README_files/figure-html/unnamed-chunk-5-1.png)<!-- -->
+![](man/figures/unnamed-chunk-5-1.png)<!-- -->
 
 (Sequence) Logo plots ([Schneider & Stephens 1990](https://academic.oup.com/nar/article-abstract/18/20/6097/1141316)) are typically used in bioinformatics as a way to visually demonstrate how well a sequence of nucleotides or amino acids are preserved in a certain region.
 
@@ -93,7 +92,7 @@ ggplot(data = ggfortify(sequences, peptide, method="shannon")) +
  theme(legend.position = "bottom") 
 ```
 
-![](README_files/figure-html/unnamed-chunk-6-1.png)<!-- -->
+![](man/figures/unnamed-chunk-6-1.png)<!-- -->
 
 ## Other variants
 
@@ -109,7 +108,7 @@ ggplot(data = ggfortify(sequences, peptide, method="shannon")) +
  theme(legend.position = "bottom") 
 ```
 
-![](README_files/figure-html/unnamed-chunk-7-1.png)<!-- -->
+![](man/figures/unnamed-chunk-7-1.png)<!-- -->
 
 Using the classic variant of alignment results in a stacked barchart of amino acids by position:
 
@@ -123,7 +122,7 @@ ggplot(data = ggfortify(sequences, peptide, method="shannon")) +
  theme(legend.position = "bottom") 
 ```
 
-![](README_files/figure-html/unnamed-chunk-8-1.png)<!-- -->
+![](man/figures/unnamed-chunk-8-1.png)<!-- -->
 
 
 ## Implementation details 
@@ -183,7 +182,7 @@ seq_info %>%
  facet_wrap(~position, ncol = 12)
 ```
 
-![](README_files/figure-html/unnamed-chunk-11-1.png)<!-- -->
+![](man/figures/unnamed-chunk-11-1.png)<!-- -->
 
 
 ## Available alphabets
@@ -199,7 +198,7 @@ alphabet %>%
  theme(aspect.ratio = 1)
 ```
 
-![](README_files/figure-html/unnamed-chunk-12-1.png)<!-- -->
+![](man/figures/unnamed-chunk-12-1.png)<!-- -->
 
 Besides the default alphabet, the fonts Comic Sans, xkcd, and braille (for 3d printing) are implemented:
 
@@ -212,7 +211,7 @@ alphabet_comic %>%
  ggtitle("Comic Sans")
 ```
 
-![](README_files/figure-html/unnamed-chunk-13-1.png)<!-- -->
+![](man/figures/unnamed-chunk-13-1.png)<!-- -->
 
 ```r
 alphabet_xkcd %>% 
@@ -222,7 +221,7 @@ alphabet_xkcd %>%
  ggtitle("xkcd font")
 ```
 
-![](README_files/figure-html/unnamed-chunk-13-2.png)<!-- -->
+![](man/figures/unnamed-chunk-13-2.png)<!-- -->
 
 ```r
 alphabet_braille %>% 
@@ -232,7 +231,7 @@ alphabet_braille %>%
  ggtitle("Braille (use in 3d prints)")
 ```
 
-![](README_files/figure-html/unnamed-chunk-13-3.png)<!-- -->
+![](man/figures/unnamed-chunk-13-3.png)<!-- -->
 
 
 ## References