figs not found

lgatto · Apr 21, 2023 · 22bccfa · 22bccfa
1 parent 8a5c10f
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Showing 3 changed files with 17 additions and 5 deletions.
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -2,7 +2,7 @@ Package: RforProteomics
 Type: Package
 Title: Companion package to the 'Using R and Bioconductor for
     proteomics data analysis' publication
-Version: 1.37.3
+Version: 1.37.4
 Authors@R: c(person("Laurent", "Gatto", role=c("aut", "cre"),
                     email="laurent.gatto@uclouvain.be"),
              person("Sebastian", "Gibb", role="ctb",

diff --git a/NEWS.md b/NEWS.md
@@ -1,5 +1,9 @@
 # RforProteomics 1
 
+## Changes in version 1.37.4
+
+Using `knitr::include_graphics()` to include figures.
+
 ## Changes in version 1.37.3
 
 - I give up: remove that effing figure that is supposedly not found

diff --git a/vignettes/RProtVis.Rmd b/vignettes/RProtVis.Rmd
@@ -603,7 +603,9 @@ an1 <- function() {
 saveGIF(an1(), movie.name = "msanim1.gif")
 ```
 
-![MS animation 1](figures/msanim1.gif)
+```{r, fig.align = "center"}
+knitr::include_graphics("figures/msanim1.gif")
+```
 
 The code chunk below scrolls of a slice of retention times while
 keeping the retention time constant between 30 and 35 minutes.
@@ -623,7 +625,9 @@ an2 <- function() {
 saveGIF(an2(), movie.name = "msanim2.gif")
 ```
 
-![MS animation 2](figures/msanim2.gif)
+```{r, fig.align = "center"}
+knitr::include_graphics("figures/msanim2.gif")
+```
 
 ## The `r Biocpkg("MSnbase")` infrastructure
 
@@ -821,7 +825,9 @@ plotMsiSlice(spectra,
 par(oldPar)
 ```
 
-![mqmsi](./figures/mqmsi-1.png)
+```{r, fig.align = "center"}
+knitr::include_graphics("figures/mqmsi-1.png")
+```
 
 ## An interactive `r CRANpkg("shiny")` app for Imaging mass spectrometry
 
@@ -834,7 +840,9 @@ library("shiny")
 runGitHub("sgibb/ims-shiny")
 ```
 
-![ims-shiny screeshot](./figures/ims-shiny.png)
+```{r, fig.align = "center"}
+knitr::include_graphics("figures/ims-shiny.png")
+```
 
 # Spatial proteomics