version 1.1.3

G3viz · Aug 25, 2020 · d1384d3 · d1384d3
1 parent 9324c22
commit d1384d3
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Showing 11 changed files with 13 additions and 451 deletions.
diff --git a/.Rbuildignore b/.Rbuildignore
@@ -1,4 +1,4 @@
-visual_test
+^visual_test/$
 ^.*\.Rproj/$
 ^\.Rproj\.user/$
 ^\.travis\.yml$
@@ -15,3 +15,5 @@ visual_test
 ^\.Rproj\.user$
 ^docs$
 ^\.DS_Store$
+^examples$
+^R/proteinDomain.R$
diff --git a/.gitignore b/.gitignore
@@ -6,7 +6,10 @@ inst/doc
 packrat/lib*/
 data-raw/
 R/temp/
+R/proteinDomain.R
 inst/backup/
 inst/extdata/backup/
 inst/htmlwidgets/backup/
 inst/htmlwidgets/lib/g3Lollipop/backup/
+visual_test/
+
diff --git a/NAMESPACE b/NAMESPACE
@@ -10,7 +10,6 @@ export(hgnc2pfam)
 export(hgnc2uniprot)
 export(mapMutationTypeToMutationClass)
 export(parseProteinChange)
-export(proteinDomain)
 export(readMAF)
 export(renderG3Lollipop)
 export(uniprot2pfam)

diff --git a/NEWS.md b/NEWS.md
@@ -1,3 +1,8 @@
+## Version 1.1.3 (2020/08/24)
+  - Updated Pfam version 33.1 (date: 2020-08-24)
+  - Updated UniProt (date: 2020-08-24)
+  - add "prepare_data" folder to instruct how to create `hgnc2pfam.df.rda` data at [GitHub](https://github.com/G3viz/g3viz) ([issue 5](https://github.com/G3viz/g3viz/issues/5))
+
 ## Version 1.1.2 (2019/04/30)
   - Clear html context before adding g3lollipop to HtmlWidgets ([issue 2](https://github.com/G3viz/g3viz/issues/2)).
 

diff --git a/R/g3Lollipop.R b/R/g3Lollipop.R
@@ -62,9 +62,6 @@ g3Lollipop <- function(mutation.dat,
                        # legend factor
                        factor.col = "Mutation_Class",
                        plot.options = g3Lollipop.options(),
-                       # ---------------------
-                       domain.info = NULL,
-                       # ---------------------
                        save.png.btn = TRUE,
                        save.svg.btn = TRUE,
                        btn.style = NA,

diff --git a/R/proteinDomain.R b/R/proteinDomain.R
@@ -64,8 +64,6 @@ proteinDomain <- function(protein.length,
   domain.end.col = "End"
   #--
 
-
-
   domain.list <- list(
     length = protein.length,
     details = domain.list

diff --git a/README.md b/README.md
@@ -42,7 +42,7 @@ if("devtools" %in% rownames(installed.packages()) == FALSE){
 devtools::install_github("g3viz/g3viz")
 ```
 
-## Cite
+## Reference
 
 Guo, X., *et al*. (2020). G3viz: an R package to interactively visualize genetic mutation data using a lollipop-diagram. **Bioinformatics**, 36(3), 928-929.
 

diff --git a/man/g3Lollipop.Rd b/man/g3Lollipop.Rd
diff --git a/man/proteinDomain.Rd b/man/proteinDomain.Rd
diff --git a/prepare_data/generate_hgnc2pfam.R b/prepare_data/generate_hgnc2pfam.R
@@ -62,7 +62,7 @@ pfam_fn <- "9606.tsv.gz"
 download.file(pfam_url, pfam_fn)
 
 # --------------------------
-message("Read pfam information ...")
+message("Read Pfam information ...")
 pfam.file <- gzcon(file(pfam_fn, "r"))
 pfam.txt <- readLines(pfam.file)
-Original file line number
+Diff line change
@@ Expand Up / @@ -42,7 +42,7 @@ if("devtools" %in% rownames(installed.packages()) == FALSE){ @@
     devtools::install_github("g3viz/g3viz")
     ```
-    ## Cite
+    ## Reference
     Guo, X., *et al*. (2020). G3viz: an R package to interactively visualize genetic mutation data using a lollipop-diagram. **Bioinformatics**, 36(3), 928-929.
@@ Expand Down @@