fix paths for vignette figures

ropensci · Oct 6, 2022 · c462a8c · c462a8c
1 parent 18a631b
commit c462a8c
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Showing 14 changed files with 29 additions and 20 deletions.
diff --git a/vignettes/data_mashups.Rmd b/vignettes/data_mashups.Rmd
@@ -12,6 +12,9 @@ vignette: >
   \usepackage[utf8]{inputenc}
 ---
 
+
+
+
 ## Combining data from OToL and other sources.
 
 One of the major goals of `rotl` is to help users combine data from other
@@ -300,7 +303,7 @@ tr <- tol_induced_subtree(ott_ids = ott_in_tree)
 plot(tr)
 ```
 
-![plot of chunk subtree](figure/subtree-1.png)
+![plot of chunk subtree](fig-vignettes-subtree-1.png)
 
 ### Connect your data to the tips of your tree
 
@@ -363,7 +366,7 @@ And now we can plot the data and the tree together
 plot(tree_data)
 ```
 
-![plot of chunk unnamed-chunk-1](figure/unnamed-chunk-1-1.png)
+![plot of chunk unnamed-chunk-1](fig-vignettes-unnamed-chunk-1-1.png)
 
 ## Find external data associated with studies, trees and taxa from Open Tree
 

diff --git a/vignettes/data_mashups.Rmd.orig b/vignettes/data_mashups.Rmd.orig
@@ -12,6 +12,11 @@ vignette: >
   \usepackage[utf8]{inputenc}
 ---
 
+```{r setup, include=FALSE}
+knitr::opts_chunk$set(fig.path = "fig-vignettes-")
+```
+
+
 ## Combining data from OToL and other sources.
 
 One of the major goals of `rotl` is to help users combine data from other

diff --git a/vignettes/fig-vignettes-birds_in_a_tree-1.png b/vignettes/fig-vignettes-birds_in_a_tree-1.png
diff --git a/vignettes/fig-vignettes-eggs_in_a_funnel-1.png b/vignettes/fig-vignettes-eggs_in_a_funnel-1.png
diff --git a/vignettes/fig-vignettes-subtree-1.png b/vignettes/fig-vignettes-subtree-1.png
diff --git a/vignettes/fig-vignettes-unnamed-chunk-1-1.png b/vignettes/fig-vignettes-unnamed-chunk-1-1.png
diff --git a/vignettes/fig-vignettes-unnamed-chunk-16-1.png b/vignettes/fig-vignettes-unnamed-chunk-16-1.png
diff --git a/vignettes/fig-vignettes-unnamed-chunk-3-1.png b/vignettes/fig-vignettes-unnamed-chunk-3-1.png
diff --git a/vignettes/fig-vignettes-unnamed-chunk-8-1.png b/vignettes/fig-vignettes-unnamed-chunk-8-1.png
diff --git a/vignettes/make-vignettes.R b/vignettes/make-vignettes.R
@@ -7,20 +7,9 @@ make_vignettes <- function() {
       knitr::knit(x, output = y)
     }
   )
-  ## clean figure directory if it exists
-  if (dir.exists("vignettes/figure")) {
-    unlink("vignettes/figure/", recursive = TRUE, force = TRUE)
-  }
-  ## recreate the directory
-  dir.create("vignettes/figure")
   ## move the figures
-  figures <- list.files("figure", pattern = "\\.png$", full.names = TRUE)
+  figures <- list.files(".", pattern = "fig-vignettes-.+\\.png$", full.names = TRUE)
   res_mv <- file.rename(figures, file.path("vignettes", figures))
   stopifnot(all(res_mv))
-
-  ## remove base directory
-  unlink("figure", recursive = TRUE, force = TRUE)
-
-  ## returns TRUE is everything worked
-  invisible(!dir.exists("figure"))
+  TRUE
 }
diff --git a/vignettes/meta-analysis.Rmd b/vignettes/meta-analysis.Rmd
@@ -12,6 +12,8 @@ vignette: >
   %\VignetteEncoding{UTF-8}
 ---
 
+
+
 ## Phylogenetic Comparative Methods
 
 The development of phylogenetic comparative methods has made phylogenies and
@@ -106,7 +108,7 @@ plot(1 / sqrt(egg_data$VZr), egg_data$Zr,
 )
 ```
 
-![plot of chunk eggs_in_a_funnel](figure/eggs_in_a_funnel-1.png)
+![plot of chunk eggs_in_a_funnel](fig-vignettes-eggs_in_a_funnel-1.png)
 
 In order to use this data later on we need to first convert it to a standard
 `data.frame`. We can also convert the `animal` column (the species names) to
@@ -317,7 +319,7 @@ tr <- tol_induced_subtree(ott_id(taxa)[is_in_tree(ott_id(taxa))])
 plot(tr, show.tip.label = FALSE)
 ```
 
-<img src="figure/birds_in_a_tree-1.png" title="plot of chunk birds_in_a_tree" alt="plot of chunk birds_in_a_tree" style="display: block; margin: auto;" />
+<img src="fig-vignettes-birds_in_a_tree-1.png" title="plot of chunk birds_in_a_tree" alt="plot of chunk birds_in_a_tree" style="display: block; margin: auto;" />
 
 There are a few things to note here. First, the tree has no branch lengths.
 At present this is true for the whole of the Open Tree synthetic tree. Some

diff --git a/vignettes/meta-analysis.Rmd.orig b/vignettes/meta-analysis.Rmd.orig
@@ -12,6 +12,10 @@ vignette: >
   %\VignetteEncoding{UTF-8}
 ---
 
+```{r setup, include=FALSE}
+knitr::opts_chunk$set(fig.path = "fig-vignettes-")
+```
+
 ## Phylogenetic Comparative Methods
 
 The development of phylogenetic comparative methods has made phylogenies and

diff --git a/vignettes/rotl.Rmd b/vignettes/rotl.Rmd
@@ -12,6 +12,8 @@ vignette: >
   \usepackage[utf8]{inputenc}
 ---
 
+
+
 `rotl` provides an interface to the Open Tree of Life (OTL) API and allows users
 to query the API, retrieve parts of the Tree of Life and integrate these parts
 with other R packages.
@@ -143,7 +145,7 @@ my_tree <- tol_induced_subtree(ott_ids = resolved_names$ott_id)
 plot(my_tree, no.margin = TRUE)
 ```
 
-![plot of chunk unnamed-chunk-3](figure/unnamed-chunk-3-1.png)
+![plot of chunk unnamed-chunk-3](fig-vignettes-unnamed-chunk-3-1.png)
 
 
 ## FAQ
@@ -366,7 +368,7 @@ mono_tree <- tol_subtree(ott_id = ott_id(mono_id))
 plot(mono_tree)
 ```
 
-![plot of chunk unnamed-chunk-8](figure/unnamed-chunk-8-1.png)
+![plot of chunk unnamed-chunk-8](fig-vignettes-unnamed-chunk-8-1.png)
 
 
 ### How do I find trees from studies focused on my favourite taxa?
@@ -666,4 +668,4 @@ tr <- tol_induced_subtree(ott_id(taxa))
 plot(tr)
 ```
 
-![plot of chunk unnamed-chunk-16](figure/unnamed-chunk-16-1.png)
+![plot of chunk unnamed-chunk-16](fig-vignettes-unnamed-chunk-16-1.png)
diff --git a/vignettes/rotl.Rmd.orig b/vignettes/rotl.Rmd.orig
@@ -12,6 +12,10 @@ vignette: >
   \usepackage[utf8]{inputenc}
 ---
 
+```{r setup, include=FALSE}
+knitr::opts_chunk$set(fig.path = "fig-vignettes-")
+```
+
 `rotl` provides an interface to the Open Tree of Life (OTL) API and allows users
 to query the API, retrieve parts of the Tree of Life and integrate these parts
 with other R packages.