From e9727b7848ecbb499744fd4d24a20fb27986d4bd Mon Sep 17 00:00:00 2001 From: GitHub Actions Date: Wed, 13 Dec 2023 16:36:26 +0000 Subject: [PATCH] markdown source builds Auto-generated via {sandpaper} Source : 6e0f0bf22d90a723d869b7085f579d9d005b9d93 Branch : main Author : Naupaka Zimmerman Time : 2023-12-13 16:32:55 +0000 Message : Merge pull request #243 from sstevens2/patch-5 Removing tidyverse install from ggplot lesson --- 03-basics-factors-dataframes.md | 2 +- 06-data-visualization.md | 45 +- config.yaml | 88 -- depth.pdf | Bin 45066 -> 45066 bytes md5sum.txt | 4 +- renv.lock | 1533 ------------------------------- 6 files changed, 33 insertions(+), 1639 deletions(-) delete mode 100644 config.yaml delete mode 100644 renv.lock diff --git a/03-basics-factors-dataframes.md b/03-basics-factors-dataframes.md index 6526daf8d..1f081e645 100644 --- a/03-basics-factors-dataframes.md +++ b/03-basics-factors-dataframes.md @@ -497,7 +497,7 @@ These packages will be installed into "~/work/genomics-r-intro/genomics-r-intro/ # Installing packages -------------------------------------------------------- - Installing ggplot2 ... OK [linked from cache] -Successfully installed 1 package in 5.9 milliseconds. +Successfully installed 1 package in 6.1 milliseconds. ``` :::::::::::::::::::::::::::::::::::::::::::::::::: diff --git a/06-data-visualization.md b/06-data-visualization.md index ca53ad43e..771ba8309 100644 --- a/06-data-visualization.md +++ b/06-data-visualization.md @@ -37,7 +37,8 @@ source: Rmd Line plot enclosed in hexagon shape with ggplot2 typed beneath and www.rstudio.com at the bottom. -**`ggplot2`** is a plotting package that makes it simple to create complex plots from data in a data frame. It provides a more programmatic interface for specifying what variables to plot, how they are displayed, and general visual properties. Therefore, we only need minimal changes if the underlying data change or if we decide to change from a bar plot to a scatter plot. This helps in creating publication-quality plots with minimal amounts of adjustments and tweaking. +**`ggplot2`** is a plotting package, part of the tidyverse, +that makes it simple to create complex plots from data in a data frame. It provides a more programmatic interface for specifying what variables to plot, how they are displayed, and general visual properties. Therefore, we only need minimal changes if the underlying data change or if we decide to change from a bar plot to a scatter plot. This helps in creating publication-quality plots with minimal amounts of adjustments and tweaking. The **gg** in "**ggplot**" stands for "**G**rammar of **G**raphics," which is an elegant yet powerful way to describe the making of scientific plots. In short, the grammar of graphics breaks down every plot into a few components, namely, a dataset, a set of geoms (visual marks that represent the data points), and a coordinate system. You can imagine this is a grammar that gives unique names to each component appearing in a plot and conveys specific information about data. With **ggplot**, graphics are built step by step by adding new elements. @@ -47,33 +48,47 @@ The idea of **mapping** is crucial in **ggplot**. One familiar example is to *ma ## Installing `tidyverse` -**`ggplot2`** belongs to the [**`tidyverse`** framework](https://www.tidyverse.org/). Therefore, we will start with loading the package **`tidyverse`**. If **`tidyverse`** is not already installed, then we need to install first. If it is already installed, then we can skip the following step: +First, we need to install the `ggplot2` package. ```r -install.packages("tidyverse") # Installing tidyverse package, includes ggplot2 and other packages such as dplyr, readr, tidyr +install.packages("ggplot2") ``` -Now, let's load the `tidyverse` package: +Now, let's load the `ggplot2` package: ```r -library(tidyverse) +library(ggplot2) +``` + +We will also use some of the other tidyverse packages we used in the last episode, so we need to load them as well. + + +```r +library(readr) +library(dplyr) +``` + +```{.output} + +Attaching package: 'dplyr' +``` + +```{.output} +The following objects are masked from 'package:stats': + + filter, lag ``` ```{.output} -── Attaching core tidyverse packages ──────────────────────── tidyverse 2.0.0 ── -✔ dplyr 1.1.4 ✔ readr 2.1.4 -✔ forcats 1.0.0 ✔ stringr 1.5.1 -✔ ggplot2 3.4.4 ✔ tibble 3.2.1 -✔ lubridate 1.9.3 ✔ tidyr 1.3.0 -✔ purrr 1.0.2 -── Conflicts ────────────────────────────────────────── tidyverse_conflicts() ── -✖ dplyr::filter() masks stats::filter() -✖ dplyr::lag() masks stats::lag() -ℹ Use the conflicted package () to force all conflicts to become errors +The following objects are masked from 'package:base': + + intersect, setdiff, setequal, union ``` + + As we can see from above output **`ggplot2`** has been already loaded along with other packages as part of the **`tidyverse`** framework. ## Loading the dataset diff --git a/config.yaml b/config.yaml deleted file mode 100644 index d35bbb686..000000000 --- a/config.yaml +++ /dev/null @@ -1,88 +0,0 @@ -#------------------------------------------------------------ -# Values for this lesson. -#------------------------------------------------------------ - -# Which carpentry is this (swc, dc, lc, or cp)? -# swc: Software Carpentry -# dc: Data Carpentry -# lc: Library Carpentry -# cp: Carpentries (to use for instructor training for instance) -# incubator: The Carpentries Incubator -carpentry: 'dc' - -# Overall title for pages. -title: 'Intro to R and RStudio for Genomics' - -# Date the lesson was created (YYYY-MM-DD, this is empty by default) -created: '2018-03-12' - -# Comma-separated list of keywords for the lesson -keywords: 'software, data, lesson, The Carpentries' - -# Life cycle stage of the lesson -# possible values: pre-alpha, alpha, beta, stable -life_cycle: 'beta' - -# License of the lesson materials (recommended CC-BY 4.0) -license: 'CC-BY 4.0' - -# Link to the source repository for this lesson -source: 'https://github.com/datacarpentry/genomics-r-intro' - -# Default branch of your lesson -branch: 'main' - -# Who to contact if there are any issues -contact: 'team@carpentries.org' - -# Navigation ------------------------------------------------ -# -# Use the following menu items to specify the order of -# individual pages in each dropdown section. Leave blank to -# include all pages in the folder. -# -# Example ------------- -# -# episodes: -# - introduction.md -# - first-steps.md -# -# learners: -# - setup.md -# -# instructors: -# - instructor-notes.md -# -# profiles: -# - one-learner.md -# - another-learner.md - -# Order of episodes in your lesson -episodes: -- 00-introduction.Rmd -- 01-r-basics.Rmd -- 02-data-prelude.Rmd -- 03-basics-factors-dataframes.Rmd -- 04-bioconductor-vcfr.Rmd -- 05-dplyr.Rmd -- 06-data-visualization.Rmd -- 07-r-help.Rmd - -# Information for Learners -learners: - -# Information for Instructors -instructors: - -# Learner Profiles -profiles: - -# Customisation --------------------------------------------- -# -# This space below is where custom yaml items (e.g. pinning -# sandpaper and varnish versions) should live - - -url: 'https://datacarpentry.github.io/genomics-r-intro' -analytics: carpentries -lang: en diff --git a/depth.pdf b/depth.pdf index 6536c466f2f24abb7cbfaaa3c520a70659f28c1b..340453b6f6e675c2a533821954ebee144c8a2422 100644 GIT binary patch delta 23 ccmeBrz|{4CX@U*2nUUc{dr1(rF?#)a0At|@FaQ7m delta 23 ccmeBrz|{4CX@U*2iGkTfdr1(rF?#)a0AuC|G5`Po diff --git a/md5sum.txt b/md5sum.txt index 200e02cff..56c097adb 100644 --- a/md5sum.txt +++ b/md5sum.txt @@ -9,11 +9,11 @@ "episodes/03-basics-factors-dataframes.Rmd" "4660e67699c358bbf4aa70e5ff7b4e24" "site/built/03-basics-factors-dataframes.md" "2023-12-13" "episodes/04-bioconductor-vcfr.Rmd" "10eb69b4697d7ecb9695d36c0d974208" "site/built/04-bioconductor-vcfr.md" "2023-12-13" "episodes/05-dplyr.Rmd" "f74055bd8677338a213e0a0c6c430119" "site/built/05-dplyr.md" "2023-12-13" -"episodes/06-data-visualization.Rmd" "d17499bf239ee3eb1a3cfbb956269d32" "site/built/06-data-visualization.md" "2023-12-13" +"episodes/06-data-visualization.Rmd" "f15dac1534761a7c3108ff7373a0aab9" "site/built/06-data-visualization.md" "2023-12-13" "episodes/07-r-help.Rmd" "1a7610b0efbaebfdd03ff4540125a790" "site/built/07-r-help.md" "2023-12-13" "instructors/instructor-notes.md" "78f6fe6109a0eb19a16ec6663941da7f" "site/built/instructor-notes.md" "2023-12-13" "learners/discuss.md" "522bcb192adf6702a2e3cb2f0d1412b5" "site/built/discuss.md" "2023-12-13" "learners/reference.md" "4e0dcbc7892af6f9610d44d356e66617" "site/built/reference.md" "2023-12-13" "learners/setup.md" "a789e69f286e17497a70650fd6be7041" "site/built/setup.md" "2023-12-13" "profiles/learner-profiles.md" "60b93493cf1da06dfd63255d73854461" "site/built/learner-profiles.md" "2023-12-13" -"renv/profiles/lesson-requirements/renv.lock" "e4ad182cf33dbfa3783fb3cbbd0f9e24" "site/built/renv.lock" "2023-12-13" +"renv/profiles/lesson-requirements/renv.lock" "59c9fcecaf565fc8fb8d9d8ea3e41196" "site/built/renv.lock" "2023-12-13" diff --git a/renv.lock b/renv.lock deleted file mode 100644 index acd3af4d7..000000000 --- a/renv.lock +++ /dev/null @@ -1,1533 +0,0 @@ -{ - 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