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Custom graphics and report generation for @atlas-aai

Home Page: https://ratlas.netlify.app

R 66.04% TeX 29.86% CSS 3.33% HTML 0.17% Lua 0.59%

r rstats rmarkdown rmarkdown-template bookdown ggplot2 ggplot2-themes

ratlas's People

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hrbrmstr eipi10 rajesh06 trinker esegui jimsforks jeffreychoover jpedroza1228

ratlas's Issues

Based on my pet peeves, I've decided against changing plotting defaults automatically when the package is loaded. However, let's write a couple functions that can globally set options if someone desires (i.e., could be used in the setup chunk of an Rmd).

There should be two versions: one for theme_atlas() (#5) and one for theme_atlas_ms() (#10). These functions should:

set the default ggplot2 theme to the corresponding atlas theme
set the default color and fill scales for discreet variables to Okabe Ito
set the default color and fill scales for continuous variables to viridis
set the default font for text and label geoms to the appropriate font for the atlas theme

plotting vignette

Create a vignette showcasing how to create atlas themed ggplot2 plots. Should include how to use:

theme_atlas() (#5)
theme_atlas_ms() (#10)
palette OkabeIto
palette atlas
theme setting functions (#11)

Should probably also begin with a brief section directing users to general ggplot2 resources, for those who aren't as familiar with ggplot2. Some ideas, but feel free to add others you have come across:

data viz from my workshop (https://tidy-ds.wjakethompson.com/days/day1/visualize/)
data viz from R4DS (https://r4ds.had.co.nz/data-visualisation.html)
data viz from Kieran Healy (http://socviz.co)

Update deprecated `dplyr::across()` functionality

The `...` argument of `across()` is deprecated as of dplyr 1.1.0.
Supply arguments directly to `.fns` through an anonymous function instead.

  # Previously
  across(a:b, mean, na.rm = TRUE)

  # Now
  across(a:b, \(x) mean(x, na.rm = TRUE))

Release ratlas 1.0.0

Prepare for release:

Submit to CRAN:

usethis::use_version("major")
Update cran-comments.md
devtools::submit_cran()
Approve email

Wait for CRAN...

Installation issue

remotes::install_github("atlas-aai/ratlas")

Error: Failed to install 'unknown package' from GitHub: HTTP error 404. No commit found for the ref master Did you spell the repo owner (atlas-aai) and repo name (ratlas) correctly? - If spelling is correct, check that you have the required permissions to access the repo.

xaringan template

For creating slide decks in Rmd.

Read about xaringan here.

Documentation (in a xaringan presentation) here.

See example custom themes already inside the xaringan package here.

report writing vignette

This vignette should demonstrate how to use ratlas to write reports.

Create new project using the "new project" template
Structure the project directories using the here package (see example usage here).
- R/ - for analysis scripts
- data-raw/ - for raw data files
- data/ - for cleaned data, or intermediate data files
- output/ - for final output files to be read into report, if not calculated in the report directly
Setup chunk
- loading package in reproducible way
- setting ggplot2 themes (see #11)
Create and cross reference tables
Create and cross reference figure
Using in line R code to dynamically populate values in the document
Combining words using knitr::combine_words()
Turning numbers into words using the english package

figure accessibility

from MK--

"In prepping a bunch of slide decks for presentations at conferences with stringent accessibility criteria, I ran into a case where we had to rebuild a graph originally generated in r by hand-entering the stats into excel and reproducing the graph. This was the best path toward getting the figure to meet accessibility criteria, rather than writing a long paragraph of alt text that didn’t conform to certain standard sequencing of information. This experience made me think R&P might want to consider extra commands in their scripts for some types of figures so we can get data like that in a little table that easily reads into excel. In this case it was clustered bar graphs showing percentages, if that helps the idea become more concrete. I can see how other graphs would be hard to reproduce in tabular form that excel would know what to do with.

I don’t have a particular solution or goal – just handing it off for consideration."

render tech reports

Should follow the same structure as functions for topicguide_docx, but for pdf tech reports. The latex template can be found in the IE Usage report repo.

custom ggplot2 theme

I would like to have a custom atlas ggplot2 theme that we can add to all our graphics with something like

+ theme_atlas()

My ideal look would be similar to theme_ipsum() from hrbrthemes, so that's probably a good place to start in terms of how to create a theme. He also has examples of how to write tests for these functions, so we will want to mimic that as well. We'll want to make some modifications to this. For example, in theme_ipsum axis title are not centered by default, and have a smaller font and the axis text. It would also be good to have the legend be at the bottom of the plot by default.

In addition, I'm hoping you can google around and figure out how to set a default color palette. I ideally, we would use palette_OkabeIto from the colorblindr package for discrete scales, and viridis from viridisLite for continuous scales. I feel like I've seen somewhere how to change the default color scales, but I can't remember now.

What I'm hoping for is that this:

library(tidyverse)
library(ratlas)

ggplot(mtcars, aes(x = mpg, y = disp)) +
  geom_point(aes(color = factor(cyl))) +
  theme_atlas()

Will do the same thing as:

library(tidyverse)
library(hrbrthemes)
library(colorblindr)

ggplot(mtcars, aes(x = mpg, y = disp)) +
  geom_point(aes(color = factor(cyl))) +
  scale_color_OkabeIto() +
  theme_ipsum(axis_title_just = "c",
              axis_title_size = 12,
              axis_text_size = 10) +
  theme(legend.position = "bottom")

^{Created on 2019-05-15 by the reprex package (v0.2.1)}

images not rendering without fig.alt

Images don't render in HTML document if alt text isn't provided in the fig.alt parameter. Images should render with fig.alt defaulting to fig.cap if alt text is not provided.

cover sheet for pdf topic guide

IDEA:

separate latex template for cover sheet.
include template .Rmd file in project for cover sheet
wrapper function for rmarkdown::render that renders both cover sheet and topic guide, then binds together
in project template Rmd, add yaml field that changes the binding of the knit button