Merge pull request #149 from /issues/147-ragg

Add ragg dependency

.Rbuildignore

@@ -16,4 +16,5 @@
 ^data-raw$
 ^\.bumpversion\.cfg$
 
-inst/rmd/rnasum.html
+^inst/rmd/rnasum.html$
+inst/rmd/html

DESCRIPTION

@@ -47,6 +47,7 @@ Imports:
     plotly,
     preprocessCore,
     purrr,
+    ragg,
     RCircos,
     readr,
     rlang,

deploy/conda/recipe/meta.yaml

@@ -30,7 +30,7 @@ requirements:
     - r-ggforce
     - r-ggplot2
     - r-glue
-    - umccr::r-gpgr
+    - r-ragg
     - r-here
     - r-htmltools
     - r-htmlwidgets
@@ -70,7 +70,7 @@ requirements:
     - r-ggforce
     - r-ggplot2
     - r-glue
-    - umccr::r-gpgr
+    - r-ragg
     - r-here
     - r-htmltools
     - r-htmlwidgets

inst/rmd/rnasum.Rmd

@@ -63,9 +63,9 @@ knitr::knit_hooks$set(timeit = local({
 knitr::opts_chunk$set(timeit = TRUE, echo = FALSE)
 ```
 
-```{r echo=TRUE, message=FALSE}
-#source(here::here("inst/rmd/params/pd.R")) # for use with 'Run All Chunks Above'
-#source(here::here("inst/rmd/params/sk.R")) # for use with 'Run All Chunks Above'
+```{r echo=FALSE, message=FALSE}
+# source(here::here("inst/rmd/params/pd.R")) # for use with 'Run All Chunks Above'
+# source(here::here("inst/rmd/params/sk.R")) # for use with 'Run All Chunks Above'
 
 # start with more exotic pkgs, then get to core ones
 {
@@ -1063,8 +1063,10 @@ for (dataset in names(ref_dataset.list)) {
   ##### Get genes genomic coordiantes
   ##### Limit genes annotation to those genes for which sample expression measurements are available
   gene_info <- tx_gene_id_105 |>
-    dplyr::select("GENEID", "GENEBIOTYPE", "GENENAME", "SEQNAME",
-        "GENESEQSTART", "GENESEQEND") |>
+    dplyr::select(
+      "GENEID", "GENEBIOTYPE", "GENENAME", "SEQNAME",
+      "GENESEQSTART", "GENESEQEND"
+    ) |>
     dplyr::rename("ENSEMBL" = "GENEID", "SYMBOL" = "GENENAME") |>
     dplyr::filter(.data$ENSEMBL %in% data.df$ENSEMBL)