update pkgdown

Zilong-Li · May 23, 2024 · be05142 · be05142
1 parent 76f9a62
commit be05142
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Showing 9 changed files with 40 additions and 78 deletions.
diff --git a/Makefile b/Makefile
@@ -8,9 +8,9 @@ rd:
 	Rscript -e 'roxygen2::roxygenise(".")'
 
 readme:
+	Rscript -e 'rmarkdown::render("README.Rmd")'
 	Rscript -e 'pkgdown::build_site()'
 	Rscript -e 'pkgdown::build_articles()'
-	Rscript -e 'rmarkdown::render("README.Rmd")'
 
 readme2:
 	Rscript -e 'rmarkdown::render("README.Rmd", "html_document")'

diff --git a/README.Rmd b/README.Rmd
@@ -93,14 +93,6 @@ par(mar=c(5,5,2,2), cex.lab = 2)
 vcfplot(res, col = 2,cex = 2, lwd = 3, type = "b")
 ```
 
-```r
-res <- vcfcomp(test = rawvcf, truth = phasedvcf,
-               stats = "f1", region = "chr21:5100000-6000000", 
-               by.sample = T)
-par(mar=c(5,5,2,2), cex.lab = 2)
-vcfplot(res, cex = 2, lwd = 3, type = "b", which.sample = 1:3)
-```
-
 ```{r pse}
 res <- vcfcomp(test = rawvcf, truth = phasedvcf,
                stats = "pse",
@@ -120,7 +112,7 @@ Want to summarize variants discovered by genotype caller e.g. GATK? `vcfsummary`
 
 ```{r summary_sm}
 res <- vcfsummary(rawvcf,"chr21:10000000-10010000")
-vcfplot(res, pop = popfile, col = 1:5, main = "Number of SNP & INDEL variants per population")
+vcfplot(res, pop = popfile, col = 1:5, main = "Number of SNP & INDEL variants")
 ```
 
 **Complex structure variants**

diff --git a/README.md b/README.md
@@ -104,14 +104,6 @@ vcfplot(res, col = 2,cex = 2, lwd = 3, type = "b")
 
 <img src="man/figures/README-r2-1.png" width="100%" />
 
-``` r
-res <- vcfcomp(test = rawvcf, truth = phasedvcf,
-               stats = "f1", region = "chr21:5100000-6000000", 
-               by.sample = T)
-par(mar=c(5,5,2,2), cex.lab = 2)
-vcfplot(res, cex = 2, lwd = 3, type = "b", which.sample = 1:3)
-```
-
 ``` r
 res <- vcfcomp(test = rawvcf, truth = phasedvcf,
                stats = "pse",
@@ -136,7 +128,7 @@ Want to summarize variants discovered by genotype caller e.g. GATK?
 
 ``` r
 res <- vcfsummary(rawvcf,"chr21:10000000-10010000")
-vcfplot(res, pop = popfile, col = 1:5, main = "Number of SNP & INDEL variants per population")
+vcfplot(res, pop = popfile, col = 1:5, main = "Number of SNP & INDEL variants")
 ```
 
 <img src="man/figures/README-summary_sm-1.png" width="100%" />

diff --git a/docs/index.html b/docs/index.html
diff --git a/docs/pkgdown.yml b/docs/pkgdown.yml
@@ -3,5 +3,5 @@ pkgdown: 2.0.9
 pkgdown_sha: ~
 articles:
   concordance-of-two-vcf-files: concordance-of-two-vcf-files.html
-last_built: 2024-05-22T16:52Z
+last_built: 2024-05-23T15:50Z
 
diff --git a/docs/reference/figures/README-dp-1.png b/docs/reference/figures/README-dp-1.png
diff --git a/docs/reference/figures/README-summary_sm-1.png b/docs/reference/figures/README-summary_sm-1.png
diff --git a/docs/search.json b/docs/search.json
diff --git a/man/figures/README-summary_sm-1.png b/man/figures/README-summary_sm-1.png