From ffb47975500673710c6f62e39c94695f7602e716 Mon Sep 17 00:00:00 2001
From: Christian Krause <christian.krause@idiv.de>
Date: Mon, 3 Jun 2019 14:27:37 +0200
Subject: [PATCH] adds plots with R
- new image sub-directory layout
- updates README instructions
---
.gitignore | 3 ++-
.spelling | 4 +++
README.md | 35 ++++++++++++++++++-------
chapter-3-results.md | 2 +-
chapter-4-discussion.md | 9 ++++++-
img/Makefile | 24 ++++++++++-------
img/graph/Makefile | 20 ++++++++++++++
img/{ => graph}/git-remote-commands.dot | 0
img/plot/Makefile | 20 ++++++++++++++
img/plot/results.R | 9 +++++++
img/plot/results.csv | 6 +++++
results.csv | 3 ---
12 files changed, 109 insertions(+), 26 deletions(-)
create mode 100644 img/graph/Makefile
rename img/{ => graph}/git-remote-commands.dot (100%)
create mode 100644 img/plot/Makefile
create mode 100644 img/plot/results.R
create mode 100644 img/plot/results.csv
delete mode 100644 results.csv
diff --git a/.gitignore b/.gitignore
index ff2f188..51dd931 100644
--- a/.gitignore
+++ b/.gitignore
@@ -1,2 +1,3 @@
*.pdf
-img/*.svg
+img/graph/*.svg
+img/plot/*.svg
diff --git a/.spelling b/.spelling
index 514f348..ed0aad0 100644
--- a/.spelling
+++ b/.spelling
@@ -1,2 +1,6 @@
+csvautobooktabular
+Graphviz
+img
pandoc
+results.csv
WatsonCrick1953
diff --git a/README.md b/README.md
index 8761bec..bf6ad05 100644
--- a/README.md
+++ b/README.md
@@ -4,22 +4,37 @@ Change to Document Title Here
Building
--------
-Build the PDF:
+To build the PDF, just type `make`. Make already does incremental compilation,
+i.e. it re-compiles only those targets whose sources changed. If you want to
+watch for changes and automatically run `make` when something changes, use
+[watchexec][]:
```
-make title.pdf
+watchexec make
```
+The `watchexec` tool honors `.gitignore`.
+
### Requirements
-Required:
+These requirements are all more or less optional or replaceable. If you want to
+build the template PDF, you need these dependencies:
+
+- [git][]
+- [pandoc and pandoc-citeproc][pandoc]
+- LaTeX, either through **texlive** or **MiKTeX**
+- GNU **make**
+- [graphviz][]
+- R including the packages **data.table**, **tidyverse** and **svglite**
+- [watchexec][]
+- [markdown-spellcheck][]
-- [git](https://git-scm.com/downloads)
-- [pandoc, pandoc-citeproc](https://pandoc.org/installing.html)
-- LaTeX, either texlive or MiKTeX
-- make
+**Note:** On MS Windows, it might be helpful using [chocolatey][].
-Optional:
-- [graphviz](https://graphviz.gitlab.io/download/)
-- [watchexec](https://github.com/watchexec/watchexec/releases)
+[chocolatey]: https://chocolatey.org/
+[git]: https://git-scm.com/downloads
+[graphviz]: https://graphviz.gitlab.io/download/
+[markdown-spellcheck]: https://www.npmjs.com/package/markdown-spellcheck
+[pandoc]: https://pandoc.org/installing.html
+[watchexec]: https://github.com/watchexec/watchexec/releases
diff --git a/chapter-3-results.md b/chapter-3-results.md
index b1efb97..734a639 100644
--- a/chapter-3-results.md
+++ b/chapter-3-results.md
@@ -14,6 +14,6 @@ You can automatically insert tables from your results if you store them in CSV.
\begin{table}
\centering
- \csvautobooktabular{results.csv}
+ \csvautobooktabular{img/plot/results.csv}
\caption{These are my super significant results.}
\end{table}
diff --git a/chapter-4-discussion.md b/chapter-4-discussion.md
index 2e06c71..ae3a79e 100644
--- a/chapter-4-discussion.md
+++ b/chapter-4-discussion.md
@@ -1,5 +1,12 @@
Discussion
==========
+You can add flow charts produced with Graphviz as in figure \ref{flowchart}.
+Note how you inline the \LaTeX\ references.
+
+work.\label{flowchart}](img/graph/git-remote-commands.svg)
+
+See these awesome, auto-generated plot in figure \ref{plot}.
+
+
diff --git a/img/Makefile b/img/Makefile
index dc8bfbf..27fce70 100644
--- a/img/Makefile
+++ b/img/Makefile
@@ -1,20 +1,24 @@
-SOURCES_DOT = $(wildcard *.dot)
+default: all
-OBJECTS_DOT_SVG = $(SOURCES_DOT:.dot=.svg)
+all: subdirs
-OBJECTS = \
- $(OBJECTS_DOT_SVG) \
+SUBDIRS = \
+ graph \
+ plot \
-all: $(OBJECTS)
+$(SUBDIRS):
+ $(MAKE) -C $@
-$(OBJECTS):
-
-%.svg: %.dot
- dot -Tsvg -o $@ $<
+subdirs: $(SUBDIRS)
clean:
- rm -f $(OBJECTS)
+ @for dir in $(SUBDIRS); do \
+ $(MAKE) -C $$dir $@; \
+ done
.PHONY: \
all \
clean \
+ default \
+ subdirs \
+ $(SUBDIRS) \
diff --git a/img/graph/Makefile b/img/graph/Makefile
new file mode 100644
index 0000000..dc8bfbf
--- /dev/null
+++ b/img/graph/Makefile
@@ -0,0 +1,20 @@
+SOURCES_DOT = $(wildcard *.dot)
+
+OBJECTS_DOT_SVG = $(SOURCES_DOT:.dot=.svg)
+
+OBJECTS = \
+ $(OBJECTS_DOT_SVG) \
+
+all: $(OBJECTS)
+
+$(OBJECTS):
+
+%.svg: %.dot
+ dot -Tsvg -o $@ $<
+
+clean:
+ rm -f $(OBJECTS)
+
+.PHONY: \
+ all \
+ clean \
diff --git a/img/git-remote-commands.dot b/img/graph/git-remote-commands.dot
similarity index 100%
rename from img/git-remote-commands.dot
rename to img/graph/git-remote-commands.dot
diff --git a/img/plot/Makefile b/img/plot/Makefile
new file mode 100644
index 0000000..12005f2
--- /dev/null
+++ b/img/plot/Makefile
@@ -0,0 +1,20 @@
+SOURCES_CSV = $(wildcard *.csv)
+
+OBJECTS_CSV_SVG = $(SOURCES_CSV:.csv=.svg)
+
+OBJECTS = \
+ $(OBJECTS_CSV_SVG) \
+
+all: $(OBJECTS)
+
+$(OBJECTS):
+
+%.svg: %.csv
+ Rscript --vanilla $*.R
+
+clean:
+ rm -f $(OBJECTS)
+
+.PHONY: \
+ all \
+ clean \
diff --git a/img/plot/results.R b/img/plot/results.R
new file mode 100644
index 0000000..14acca4
--- /dev/null
+++ b/img/plot/results.R
@@ -0,0 +1,9 @@
+library(data.table)
+library(ggplot2)
+
+data <- fread("results.csv")
+
+plot <- ggplot(data, aes(x, y)) +
+ geom_point(aes(col = cat))
+
+ggsave("results.svg", plot)
diff --git a/img/plot/results.csv b/img/plot/results.csv
new file mode 100644
index 0000000..6a9061c
--- /dev/null
+++ b/img/plot/results.csv
@@ -0,0 +1,6 @@
+cat,x,y,foo
+a,1,2,8
+b,6,3,7
+c,7,4,5
+d,2,5,1
+e,1,8,7
diff --git a/results.csv b/results.csv
deleted file mode 100644
index 88700c7..0000000
--- a/results.csv
+++ /dev/null
@@ -1,3 +0,0 @@
-a,b,c
-1,2,3
-4,5,6
--
GitLab