[CHNOSZ-commits] r157 - in pkg/CHNOSZ: . inst vignettes
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Fri Feb 17 03:51:35 CET 2017
Author: jedick
Date: 2017-02-17 03:51:34 +0100 (Fri, 17 Feb 2017)
New Revision: 157
Added:
pkg/CHNOSZ/vignettes/rubisco.svg
Modified:
pkg/CHNOSZ/DESCRIPTION
pkg/CHNOSZ/inst/NEWS
pkg/CHNOSZ/vignettes/anintro.Rmd
Log:
anintro.Rmd: use premade rubisco.svg
Modified: pkg/CHNOSZ/DESCRIPTION
===================================================================
--- pkg/CHNOSZ/DESCRIPTION 2017-02-17 00:31:54 UTC (rev 156)
+++ pkg/CHNOSZ/DESCRIPTION 2017-02-17 02:51:34 UTC (rev 157)
@@ -1,6 +1,6 @@
Date: 2017-02-17
Package: CHNOSZ
-Version: 1.0.8-46
+Version: 1.0.8-47
Title: Chemical Thermodynamics and Activity Diagrams
Author: Jeffrey Dick
Maintainer: Jeffrey Dick <j3ffdick at gmail.com>
Modified: pkg/CHNOSZ/inst/NEWS
===================================================================
--- pkg/CHNOSZ/inst/NEWS 2017-02-17 00:31:54 UTC (rev 156)
+++ pkg/CHNOSZ/inst/NEWS 2017-02-17 02:51:34 UTC (rev 157)
@@ -1,4 +1,4 @@
-CHANGES IN CHNOSZ 1.0.8-46 (2017-02-17)
+CHANGES IN CHNOSZ 1.0.8-47 (2017-02-17)
---------------------------------------
DOCUMENTATION:
Modified: pkg/CHNOSZ/vignettes/anintro.Rmd
===================================================================
--- pkg/CHNOSZ/vignettes/anintro.Rmd 2017-02-17 00:31:54 UTC (rev 156)
+++ pkg/CHNOSZ/vignettes/anintro.Rmd 2017-02-17 02:51:34 UTC (rev 157)
@@ -71,48 +71,9 @@
dpi <- 72
}
-## pandoc error is caused by non-existent figure in rubisco_svg chunk when RSVGTipsDevice is not available,
-## so extend knitr's hook_plot_custom to check for existence of figure file 20170216
-## first, we need to copy a couple of knitr's utility functions
-# if LHS is NULL, return the RHS
-`%n%` = function(x, y) if (is.null(x)) y else x
-# recycle some plot options such as fig.cap, out.width/height, etc when there
-# are multiple plots per chunk
-.recyle.opts = c('fig.cap', 'fig.scap', 'fig.env', 'fig.pos', 'fig.subcap',
- 'out.width', 'out.height', 'out.extra', 'fig.link')
-# when passing options to plot hooks, reduce the recycled options to scalars
-reduce_plot_opts = function(options) {
- i = options$fig.cur %n% 1L
- for (o in .recyle.opts) {
- v = options[[o]]
- if ((n <- length(v)) == 0) next
- if ((j <- i %% n) == 0) j = n
- options[o] = list(v[j])
- }
- options
-}
-hook_plot_custom_checkfile = function(before, options, envir){
- if (before) return() # run hook after the chunk
- if (options$fig.show == 'hide') return() # do not show figures
-
- ext = options$fig.ext %n% dev2ext(options$dev)
- hook = knit_hooks$get('plot')
-
- # do not show non-existent figure
- if (!file.exists(fig_path(ext, options, 1))) return()
-
- n = options$fig.num
- if (n == 0L) n = options$fig.num = 1L # make sure fig.num is at least 1
- res = unlist(lapply(seq_len(n), function(i) {
- options$fig.cur = i
- hook(fig_path(ext, options, i), reduce_plot_opts(options))
- }), use.names = FALSE)
- paste(res, collapse = '')
-}
-
## http://stackoverflow.com/questions/23852753/knitr-with-gridsvg
## Set up a chunk hook for manually saved plots.
-knit_hooks$set(custom.plot = hook_plot_custom_checkfile)
+knit_hooks$set(custom.plot = hook_plot_custom)
## hook to change <img /> to <embed /> -- required for interactive SVG
hook_plot <- knit_hooks$get("plot")
@@ -131,28 +92,6 @@
}
})
timeit <- NULL
-
-## 20170216 workaround for R CMD check warning only on Windows (R-Forge, winbuilder):
-# * checking re-building of vignette outputs ... WARNING
-# Error in re-building vignettes:
-# ...
-# Warning in get_engine(options$engine) :
-# Unknown language engine 'marginfigure' (must be registered via knit_engines$set()).
-##
-## from html.R in tufte package:
-knitr::knit_engines$set(marginfigure = function(options) {
- options$type = 'marginnote'
- if (is.null(options$html.tag)) options$html.tag = 'span'
- options$html.before = marginnote_html()
- eng_block = knitr::knit_engines$get('block')
- eng_block(options)
-})
-marginnote_html = function(text = '', icon = '⊕') {
- sprintf(paste0(
- '<label for="tufte-mn-" class="margin-toggle">%s</label>',
- '<input type="checkbox" id="tufte-mn-" class="margin-toggle">%s'
- ), icon, text)
-}
```
# First steps
@@ -1137,9 +1076,11 @@
Then, we calculate `r zc` from the formulas of the proteins.
Next, point symbols are assigned according to domain (Archaea, Bacteria, Eukaryota); numbers inside the symbols show the ordering of *T*<sub>opt</sub> in three temperature ranges (0--35 °C, 37.5--60 °C, and 65--100 °C).
-<!--
-```{r rubisco_svg, fig.margin=TRUE, fig.width=4, fig.height=4, small.mar=TRUE, out.width="100%", fig.keep='none', fig.ext='svg', custom.plot=TRUE, embed.tag=TRUE, echo=FALSE, results="hide", message=FALSE, fig.cap='Average oxidation state of carbon in Rubisco compared with optimal growth temperature of organisms. **This is an interactive image.** Move the mouse over the points to show the names of the organisms, and click to open a reference in a new window. (Made using [RSVGTipsDevice](https://cran.r-project.org/package=RSVGTipsDevice) with code that can be found in the source of this document.)', cache=TRUE, timeit=timeit}
-#if(suppressWarnings(require(RSVGTipsDevice))) {
+```{r rubisco_svg, echo=FALSE, results="hide", fig.margin=TRUE, fig.width=4, fig.height=4, small.mar=TRUE, out.width="100%", fig.ext='svg', custom.plot=TRUE, embed.tag=TRUE, fig.cap='Average oxidation state of carbon in Rubisco compared with optimal growth temperature of organisms. **This is an interactive image.** Move the mouse over the points to show the names of the organisms, and click to open a reference in a new window. (Made using [RSVGTipsDevice](https://cran.r-project.org/package=RSVGTipsDevice) with code that can be found in the source of this document.)'}
+## copies the premade SVG image to the knitr figure path
+file.copy("rubisco.svg", fig_path(".svg"))
+## the code for making the SVG image -- not "live" in the vignette because RSVGTipsDevice isn't available on Windows
+#if(require(RSVGTipsDevice)) {
# datfile <- system.file("extdata/cpetc/rubisco.csv", package = "CHNOSZ")
# fastafile <- system.file("extdata/fasta/rubisco.fasta", package = "CHNOSZ")
# dat <- read.csv(datfile)
@@ -1152,7 +1093,7 @@
# col <- match(dat$domain, c("A", "B", "E")) + 1
# # because the tooltip titles in the SVG file are shown by recent browsers,
# # we do not need to draw the tooltips explicitly, so set toolTipMode=0
-# devSVGTips(fig_path('.svg'), toolTipMode=0, title="Rubisco")
+# devSVGTips("rubisco.svg", toolTipMode=0, title="Rubisco")
# par(cex=1.4)
# # unfortunately, plotmath can't be used with devSVGTips,
# # so axis labels here don't contain italics.
@@ -1173,9 +1114,8 @@
# dev.off()
#}
```
--->
-```{r rubisco_ZC, fig.margin=TRUE, fig.width=4, fig.height=4, small.mar=TRUE, dpi=dpi, out.width="100%", echo=FALSE, message=FALSE, fig.cap="Average oxidation state of carbon in Rubisco compared with optimal growth temperature of organisms.", cache=TRUE, pngquant=pngquant, timeit=timeit}
-#if(!suppressWarnings(require(RSVGTipsDevice))) {
+
+```{r rubisco_ZC, fig.keep="none"}
datfile <- system.file("extdata/cpetc/rubisco.csv", package = "CHNOSZ")
fastafile <- system.file("extdata/fasta/rubisco.fasta", package = "CHNOSZ")
dat <- read.csv(datfile)
@@ -1193,10 +1133,7 @@
abline(v = c(36, 63), lty = 2, col = "grey")
legend("topright", legend = c("Archaea", "Bacteria", "Eukaryota"),
pch = c(2, 1, 0), col = 2:4, pt.cex = 2)
-#}
```
-```{r rubisco_ZC, eval=FALSE, echo=2:18}
-```
Let's look at the different ways of representing the chemical compositions of the proteins.
<span style="color:green">`protein.basis()`</span> returns the stoichiometry for the formation reaction of each proteins.
Added: pkg/CHNOSZ/vignettes/rubisco.svg
===================================================================
(Binary files differ)
Property changes on: pkg/CHNOSZ/vignettes/rubisco.svg
___________________________________________________________________
Added: svn:mime-type
+ image/svg
More information about the CHNOSZ-commits
mailing list