diff --git a/DESCRIPTION b/DESCRIPTION index eb6bf05..49cee78 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -41,6 +41,6 @@ Imports: Suggests: knitr, rmarkdown -VignetteBuilder: rmarkdown +VignetteBuilder: knitr RoxygenNote: 7.2.3 LazyData: true diff --git a/NEWS.md b/NEWS.md index dfb98be..7a7ad52 100644 --- a/NEWS.md +++ b/NEWS.md @@ -5,13 +5,10 @@ # ogrdbstats 0.5.1 -* Fixed a problem which prevented haplotyping plots from being produced. -* Fixed various issues with report formatting - -* Added support for recent versions of IgDiscover, which now uses a AIRR format for filtered.tsv -* Added automatic sequence gapping for the AIRR format column sequence_alignment, should it not be gapped (this was required for IgDIscover support) -* Fixed the creation of output files where the input file included more than one period in its name +* Added support for recent versions of IgDiscover, which now uses AIRR format for filtered.tsv. +* The AIRR format sequence column may now be supplied ungapped, in which case ogrdbstats will gap the sequences before use. +* Output files will be named correctly even if the input file includes more than one period in its name. # ogrdbstats 0.5.2 -* Fixed an error in the CRAN package checks: `grobs` must be a single grob or a list of grobs, not a list. \ No newline at end of file +* Changed the Vignette builder from knitr to rmarkdown to avoid an error during package creation. \ No newline at end of file diff --git a/vignettes/using_ogrdbstats.Rmd b/vignettes/using_ogrdbstats.Rmd index de072a1..cb5f8b3 100644 --- a/vignettes/using_ogrdbstats.Rmd +++ b/vignettes/using_ogrdbstats.Rmd @@ -289,7 +289,7 @@ rd = suppressMessages( barplot_grobs = make_barplot_grobs(rd$input_sequences, rd$genotype_db, rd$inferred_seqs, rd$genotype, 'V', rd$calculated_NC) base_grobs = make_novel_base_grobs(rd$inferred_seqs, rd$input_sequences, 'V', FALSE) -gridExtra::grid.arrange(grobs=list(barplot_grobs[3][[1]], base_grobs$end[1][[1]], +gridExtra::grid.arrange(grobs=list(barplot_grobs[2][[1]], base_grobs$end[1][[1]], base_grobs$conc[1][[1]]),ncol=1)