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Add GC content function for plot. #151
base: improve-pkgdown-code-chunk-label
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Commits on Feb 2, 2021
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flip_nicely -> flip_by_links; redo strand after sublinks to links; a-…
…b = b-a for link grouping; fixes #29
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Merge pull request #38 from thackl/misc-issues
various smaller fixes and improvements
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Commits on Feb 8, 2021
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make "genes" the first argument of gggenomes() - more intuitive; Supp…
…ort paths as gggenomes() arguments
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Merge pull request #37 from thackl/revise-smart-read
improve smart-read backend with new mapping of defined formats, extensions, context and parsers
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Merge pull request #41 from thackl/gggenomes-gene-centric-api
make genes the first arguement of gggenomes for more intuitive usage. gggenomes() also reads files now
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Merge pull request #45 from thackl/multi-locus-focus
Made it possible to focus on several regions from the same parent sequence at once
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Merge pull request #50 from thackl/locate-and-position-examples
Added locate - like focus, but add loci as track instead of zoom; added position_* examples
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Merge pull request #56 from thackl/scale-x
Added scale_x_bp() as default x-scale
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Commits on Apr 15, 2021
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y-coords now go from 0 (bottom) to n (top), but bins are mapped in re…
…verse so still plotted from top to bottom
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bins compute ymin and ymax for wrapped bins, geom_bin_label can use t…
…hose for top/bottom alignment
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Commits on Apr 16, 2021
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Merge pull request #58 from thackl/scale-y
y-coords not reversed anymore, but instead bin positions are mapped reversely to numeric y-coordinates to arrange bins from top to bottom. Fixes #55
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Merge pull request #60 from thackl/get-started
first sections of "get-started" doc, and geom_wiggle
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various small improvements and fixes for reading gff files, including…
… support for gtf/gff2
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Merge pull request #68 from thackl/gff-issues-2
follow-up on improvements and fixes for reading gff files, including support for gtf/gff2
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Merge pull request #71 from thackl/fix_cds_in_write_gff3
Fix collapsed CDS in write_gff3
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Merge pull request #76 from thackl/issues-200821
Allow drawing all links among all genomes
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Merge pull request #81 from thackl/issues-200912
fix focus and flip bug plus some flip doc
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Merge pull request #84 from thackl/focus-loci-order
retain order of input sequences for loci in focus
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Commits on Oct 21, 2021
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Merge pull request #92 from nschan/import-decipher-synteny-as-links
Import DECIPHER synteny as links
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Commits on Nov 6, 2021
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Instead of png image, svg image looks better. Therefore, the svg image was selected from the existing files and its size was adjusted.
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Commits on Nov 7, 2021
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Merge pull request #97 from frknc/patch-1
Change logo in REAME from PNG to SVG Somewhere in the back of my had I had this notion that I generated the PNG specifically because github doesn't handle SVGs properly / I though github would not handle SVG properly. But based on some quick googling, this does not seem to be the case. So this seems like a good idea, thanks wink !
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Commits on Jan 16, 2023
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Created a new function called geom_coverage. This function is documented together with geom_wiggle due to there similar nature.
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changed size to linewidth for geom_feat. ggplot2::geom_segment uses linewidth since latest update (version 3.4.0)
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Newest version of roxygen2 (7.2.3) update different documentation files automatically
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Updated geom_feat documentation
The documentation for geom_feat was still missing. A simple basic documentation explaining different options has been created.
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Commits on Jan 18, 2023
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The latest update of ggplot2 (version 3.4.0), had several changes that partly influence functions within the gggenomes package. Any line_object can no be changed in size by using `linewidth = ...` (rather than previously used `size = ...`). This change has influence on both `gggenomes::geom_feat` and `gggenomes::geom_seq`.
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Merge pull request #139 from BvAdrichem/geom_coverage
Geom coverage and geom_feat.rd update
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Commits on Mar 9, 2023
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The feats track will now automatically read/look for a `type` column within the dataframe. By abscence, it will create a ("dummy") column containing 'NA'.
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The function geom_variant was created and documented. This function will be usefull for visualization (and potentially analyzing) of VCF-files. It uses ggplot2: geom_point under the hood.
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Position_variant was created and doucemented. Position_ variant uses a ggproto object, which allows the user to plot point (from e.g. geom_variant) at different offsets based on the type of mutation.
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Newly created functions scale_color_variant and scale_shape_variant. Both used to easily create default aesthetics for color and shape for mutations.
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roxygen2: auto updated documentation
Documentation was automatically updated by roxygen2 for these two files.
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Commits on Mar 20, 2023
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Documentation update: vcf-functions
Update to the documentation of the functions, 'geom_variant'()', 'position_variant()', 'scale_color_variant()' and 'scale_shape_variant()'. + fixed smalle typo in feats.r
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smalle adjustment of text: Deletion -> del SNP -> snp Insertion -> ins
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Commits on Apr 3, 2023
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Creation of function read_vcf with documentation. Some small updates to global environment (necessary for read_vcf). Sequentially, Rd has been updated.
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Commits on May 2, 2023
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Update documentation on geom_seq, geom_feat, geom_link, gggenomes and track_info gggenomes vignette still in progress.
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Commits on Jun 13, 2023
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Updated documentation for: -geom_seq: examples no shows how to use (arguments) wrap and spacing. -geom_feat/gene_text: was lacking examples and description Created documentation for: -geom_link/gene/feat_label: Grouped these three together and referenced to other gggenomes' labeling functions -geom_seq_label: Created simple documentation with examples. -shift: Simple documentation with examples
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Merge branch 'Improved-documentation' of https://github.com/BvAdriche…
…m/gggenomes into Improved-documentation
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Commits on Jun 16, 2023
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Merge pull request #154 from BvAdrichem/Improved-documentation
Improved documentation
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Commits on Aug 2, 2023
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Fix empty attributes check in read_gff3
The original check used vectorized conditions with || and inside if. This is potentially problematic and results in errors rather than warnings starting from R version 4.2.0 Fix #156
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Commits on Oct 6, 2023
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Merge pull request #160 from thackl/138-geom-blank
fix #138 geom_blank error
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Merge pull request #157 from thackl/fix-156
Fix empty attributes check in read_gff3
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Merge pull request #162 from thackl/geom_seq_break
added geom_seq_break()
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changed Depends: to Imports: and added more explicit calls to functio…
…ns in other packages; minor fixes to examples along the way; resolves #142
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"bold" is not a valid font family this does not produce errors when I call it interactively but R CMD check produces the "invalid font type" error. Changing this to "sans" does not change the appearence of the plot for me.
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package is only listed as Suggests, anyway. See r-lib/devtools#1717
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Merge pull request #178 from thackl/ggplot-3.5.0-compatibility
Add ggplot 3.5.0 compatibility (guides and layout ggproto)
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reduce package size by replacing .fna files with .fna.fai indices, re…
…moving unnecessary data; updated examples;
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Merge pull request #168 from thackl/cran-ready
Make gggenomes ready for CRAN submission
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This is necessary from roxygen 7.3, see https://www.tidyverse.org/blog/2024/01/roxygen2-7-3-0/ and details in https://roxygen2.r-lib.org/articles/namespace.html#s3
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Fix missing \value tags in Rd files
Instances found using checkhelper::find_missing_tags() Automatic formatting applied
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Merge pull request #189 from thackl/perl-to-r
This version has just been accepted by CRAN 🎉 https://cran.r-project.org/web/packages/gggenomes/index.html
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capture unavailable web resource gracefully in vignette for CRAN comp…
…atibility. Fixes #197
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