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Add GC content function for plot. #151

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Commits on Feb 2, 2021

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Commits on Feb 6, 2021

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Commits on Feb 7, 2021

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  3. flip_nicely -> flip_by_links; redo strand after sublinks to links; a-…

    …b = b-a for link grouping; fixes #29
    thackl committed Feb 7, 2021
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  5. bump version

    thackl committed Feb 7, 2021
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  6. Merge pull request #38 from thackl/misc-issues

    various smaller fixes and improvements
    thackl authored Feb 7, 2021
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Commits on Feb 8, 2021

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  2. make "genes" the first argument of gggenomes() - more intuitive; Supp…

    …ort paths as gggenomes() arguments
    thackl committed Feb 8, 2021
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  4. Fix context for links

    iimog committed Feb 8, 2021
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  6. Fix alitv example

    iimog committed Feb 8, 2021
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  7. Merge pull request #37 from thackl/revise-smart-read

    improve smart-read backend with new mapping of defined formats, extensions, context and parsers
    thackl authored Feb 8, 2021
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  9. bump version

    thackl committed Feb 8, 2021
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  10. 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
    thackl authored Feb 8, 2021
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Commits on Feb 9, 2021

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Commits on Feb 10, 2021

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Commits on Feb 11, 2021

  1. fix wrong parser for blast

    thackl committed Feb 11, 2021
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  3. Merge pull request #45 from thackl/multi-locus-focus

    Made it possible to focus on several regions from the same parent sequence at once
    thackl authored Feb 11, 2021
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Commits on Feb 15, 2021

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  4. 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
    thackl authored Feb 15, 2021
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Commits on Feb 18, 2021

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  3. Add sessionInfo for debugging

    iimog committed Feb 18, 2021
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  4. Force re-build of docs

    iimog committed Feb 18, 2021
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  5. Force re-build of docs

    iimog committed Feb 18, 2021
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  6. Re-generate Rd files

    iimog committed Feb 18, 2021
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  7. Debug gh-action

    iimog authored Feb 18, 2021
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Commits on Feb 19, 2021

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Commits on Feb 22, 2021

  1. Remove debug action

    iimog authored Feb 22, 2021
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Commits on Apr 11, 2021

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  2. Merge pull request #56 from thackl/scale-x

    Added scale_x_bp() as default x-scale
    thackl authored Apr 11, 2021
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Commits on Apr 15, 2021

  1. y-coords now go from 0 (bottom) to n (top), but bins are mapped in re…

    …verse so still plotted from top to bottom
    thackl committed Apr 15, 2021
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  2. bins compute ymin and ymax for wrapped bins, geom_bin_label can use t…

    …hose for top/bottom alignment
    thackl committed Apr 15, 2021
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Commits on Apr 16, 2021

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  3. version bump

    thackl committed Apr 16, 2021
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  4. 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
    thackl authored Apr 16, 2021
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Commits on Apr 20, 2021

  1. Use dev version of pkgdown

    iimog committed Apr 20, 2021
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Commits on Apr 21, 2021

  1. Install dev version of ggtree

    iimog committed Apr 21, 2021
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  2. Add devtools to action

    iimog committed Apr 21, 2021
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  3. Merge pull request #59 from iimog/master

    Fix documentation problem
    iimog authored Apr 21, 2021
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Commits on Jun 1, 2021

  1. added geom_wiggle()

    thackl committed Jun 1, 2021
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  2. make genes flippable

    thackl committed Jun 1, 2021
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  3. doc fixes

    thackl committed Jun 1, 2021
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  5. Merge pull request #60 from thackl/get-started

    first sections of "get-started" doc, and geom_wiggle
    thackl authored Jun 1, 2021
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Commits on Jun 2, 2021

  1. Add Hmisc to suggests and gh action env

    Fix #61
    iimog committed Jun 2, 2021
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Commits on Aug 9, 2021

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  2. doc

    thackl committed Aug 9, 2021
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  3. various small improvements and fixes for reading gff files, including…

    … support for gtf/gff2
    thackl committed Aug 9, 2021
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  4. Merge pull request #66 from thackl/gff-issues

    Gff issues
    thackl authored Aug 9, 2021
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Commits on Aug 10, 2021

  1. add snakecase dependency

    thackl committed Aug 10, 2021
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  2. bump version

    thackl committed Aug 10, 2021
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  3. Merge pull request #68 from thackl/gff-issues-2

    follow-up on improvements and fixes for reading gff files, including support for gtf/gff2
    thackl authored Aug 10, 2021
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Commits on Aug 20, 2021

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  2. Merge pull request #71 from thackl/fix_cds_in_write_gff3

    Fix collapsed CDS in write_gff3
    thackl authored Aug 20, 2021
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Commits on Sep 12, 2021

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  2. Merge pull request #76 from thackl/issues-200821

    Allow drawing all links among all genomes
    thackl authored Sep 12, 2021
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  6. bump version

    thackl committed Sep 12, 2021
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  7. Merge pull request #81 from thackl/issues-200912

    fix focus and flip bug plus some flip doc
    thackl authored Sep 12, 2021
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Commits on Sep 14, 2021

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  2. Merge pull request #84 from thackl/focus-loci-order

    retain order of input sequences for loci in focus
    thackl authored Sep 14, 2021
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Commits on Oct 20, 2021

  1. Create synteny_to_link.R

    nschan authored Oct 20, 2021
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  2. Update synteny_to_link.R

    Cleaned up
    nschan authored Oct 20, 2021
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Commits on Oct 21, 2021

  1. Merge pull request #92 from nschan/import-decipher-synteny-as-links

    Import DECIPHER synteny as links
    thackl authored Oct 21, 2021
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Commits on Oct 27, 2021

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  5. filter gff by type and source

    thackl committed Oct 27, 2021
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Commits on Nov 4, 2021

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  2. bump version

    thackl committed Nov 4, 2021
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Commits on Nov 6, 2021

  1. logo change in readme

    Instead of png image, svg image looks better. Therefore, the svg image was selected from the existing files and its size was adjusted.
    frknc authored Nov 6, 2021
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Commits on Nov 7, 2021

  1. 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 !
    thackl authored Nov 7, 2021
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Commits on Nov 30, 2021

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Commits on Feb 1, 2022

  1. typos

    raynamharris authored Feb 1, 2022
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Commits on Mar 30, 2022

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Commits on Nov 9, 2022

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Commits on Jan 16, 2023

  1. geom_coverage

    Created a new function called geom_coverage. This function is documented together with geom_wiggle due to there similar nature.
    BvAdrichem committed Jan 16, 2023
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  2. Update geom_feat

    changed size to linewidth for geom_feat.
    ggplot2::geom_segment uses linewidth since latest update (version 3.4.0)
    BvAdrichem committed Jan 16, 2023
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  3. Update Roxygen2

    Newest version of roxygen2 (7.2.3) update different documentation files automatically
    BvAdrichem committed Jan 16, 2023
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  4. Updated geom_feat documentation

    The documentation for geom_feat was still missing. A simple basic documentation explaining different options has been created.
    BvAdrichem committed Jan 16, 2023
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Commits on Jan 18, 2023

  1. Update DESCRIPTION

    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`.
    BvAdrichem authored Jan 18, 2023
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Commits on Feb 23, 2023

  1. Merge pull request #108 from raynamharris/patch-1

    typos
    thackl authored Feb 23, 2023
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  2. Merge pull request #139 from BvAdrichem/geom_coverage

    Geom coverage and geom_feat.rd update
    thackl authored Feb 23, 2023
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  3. Update pkgdown.yaml

    r-lib/actions/setup-r branch changed to v2
    thackl authored Feb 23, 2023
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  4. Update pkgdown.yaml

    thackl authored Feb 23, 2023
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  5. Update DESCRIPTION

    thackl authored Feb 23, 2023
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  6. Update pkgdown.yaml

    unmet ggtree dependencies
    thackl authored Feb 23, 2023
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  7. Update pkgdown.yaml

    thackl authored Feb 23, 2023
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  8. Update pkgdown.yaml

    thackl authored Feb 23, 2023
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  9. Update pkgdown.yaml

    base R pipe-compatible version
    thackl authored Feb 23, 2023
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  10. Update synteny_to_link.R

    pkgdown compatibility
    thackl authored Feb 23, 2023
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  11. Update _pkgdown.yml

    synteny_to_link missing in pkgdown topics
    thackl authored Feb 23, 2023
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  12. Update synteny_to_link.R

    thackl authored Feb 23, 2023
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Commits on Mar 9, 2023

  1. Update feats.R

    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'.
    BvAdrichem committed Mar 9, 2023
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  2. geom_variant

    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.
    BvAdrichem committed Mar 9, 2023
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  3. position_variant

    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.
    BvAdrichem committed Mar 9, 2023
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  4. variant_scales

    Newly created functions scale_color_variant and scale_shape_variant. Both used to easily create default aesthetics for color and shape for mutations.
    BvAdrichem committed Mar 9, 2023
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  5. roxygen2: auto updated documentation

    Documentation was automatically updated by roxygen2 for these two files.
    BvAdrichem committed Mar 9, 2023
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Commits on Mar 20, 2023

  1. 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
    BvAdrichem committed Mar 20, 2023
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  2. Update feats.R

    BvAdrichem committed Mar 20, 2023
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  3. documentation update

    smalle adjustment of text:
    Deletion -> del
    SNP -> snp
    Insertion -> ins
    BvAdrichem committed Mar 20, 2023
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Commits on Apr 3, 2023

  1. read_vcf

    Creation of function read_vcf with documentation. Some small updates to global environment (necessary for read_vcf). Sequentially, Rd has been updated.
    BvAdrichem committed Apr 3, 2023
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Commits on Apr 12, 2023

  1. Merge pull request #144 from BvAdrichem/VCF-functions

    Vcf functions
    thackl authored Apr 12, 2023
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  3. updated man for pkgdown

    thackl committed Apr 12, 2023
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Commits on Apr 19, 2023

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Commits on May 2, 2023

  1. Updated documentation

    Update documentation on geom_seq, geom_feat, geom_link, gggenomes and track_info
    
    gggenomes vignette still in progress.
    BvAdrichem committed May 2, 2023
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  2. Update layout_genomes.Rd

    BvAdrichem committed May 2, 2023
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Commits on Jun 13, 2023

  1. documentation update

    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
    BvAdrichem committed Jun 13, 2023
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Commits on Jun 16, 2023

  1. Merge pull request #154 from BvAdrichem/Improved-documentation

    Improved documentation
    thackl authored Jun 16, 2023
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Commits on Aug 2, 2023

  1. 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
    iimog committed Aug 2, 2023
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Commits on Oct 6, 2023

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  2. Merge pull request #160 from thackl/138-geom-blank

    fix #138 geom_blank error
    thackl authored Oct 6, 2023
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  3. Merge pull request #157 from thackl/fix-156

    Fix empty attributes check in read_gff3
    thackl authored Oct 6, 2023
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  4. doc typos, etc

    thackl committed Oct 6, 2023
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Commits on Oct 12, 2023

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  2. Merge pull request #162 from thackl/geom_seq_break

    added geom_seq_break()
    thackl authored Oct 12, 2023
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  3. forgot man/geom_seq_break

    thackl committed Oct 12, 2023
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Commits on Oct 14, 2023

  1. update my email to rug

    thackl committed Oct 14, 2023
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  2. doc edits

    thackl committed Oct 14, 2023
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  4. updated front page example

    thackl committed Oct 14, 2023
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Commits on Oct 15, 2023

  1. updated geom_link() example

    thackl committed Oct 15, 2023
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  3. updated shift() example, fixes #163

    thackl committed Oct 15, 2023
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  4. changed Depends: to Imports: and added more explicit calls to functio…

    …ns in other packages; minor fixes to examples along the way; resolves #142
    thackl committed Oct 15, 2023
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  5. add tidyverse to vignette

    thackl committed Oct 15, 2023
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Commits on Oct 16, 2023

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  2. bump version

    thackl committed Oct 16, 2023
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  4. example dplyr namespace fix

    thackl committed Oct 16, 2023
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  5. more example namespace fixes

    thackl committed Oct 16, 2023
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  6. update readme

    thackl committed Oct 16, 2023
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  7. update readme

    thackl committed Oct 16, 2023
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Commits on Oct 17, 2023

  1. Remove obsolete remote

    iimog committed Oct 17, 2023
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  2. Add magrittr to Imports

    iimog committed Oct 17, 2023
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  3. Re-generate docs

    iimog committed Oct 17, 2023
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  5. Fix invalid font type error

    "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.
    iimog committed Oct 17, 2023
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  8. Use explicit TRUE instead of T

    iimog committed Oct 17, 2023
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Commits on Oct 18, 2023

  1. Fix typo in function name

    iimog committed Oct 18, 2023
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  2. Fix variable names in example

    iimog committed Oct 18, 2023
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  4. Add split_by to exports

    iimog committed Oct 18, 2023
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  6. Add reference to license file

    iimog committed Oct 18, 2023
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Commits on Nov 7, 2023

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Commits on Nov 10, 2023

  1. Fix 1/4 codoc mismatch warnings

    iimog committed Nov 10, 2023
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Commits on Nov 30, 2023

  1. Fix codoc mismatch warnings

    iimog committed Nov 30, 2023
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Commits on Dec 8, 2023

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Commits on Dec 11, 2023

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  2. Fix missing file link warnings

    iimog committed Dec 11, 2023
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Commits on Jan 3, 2024

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Commits on Jan 12, 2024

  1. Remove unused argument

    Fix #172
    iimog committed Jan 12, 2024
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Commits on Jan 16, 2024

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  3. Fix duplicate title note

    iimog committed Jan 19, 2024
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  4. Fix link to emales data

    iimog committed Jan 19, 2024
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  5. Fix non-standard directory note

    iimog committed Jan 19, 2024
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  7. Remotes not allowed on CRAN

    package is only listed as Suggests, anyway.
    See r-lib/devtools#1717
    iimog committed Jan 19, 2024
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  13. Use is() to check for class

    iimog committed Jan 19, 2024
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  2. Merge pull request #178 from thackl/ggplot-3.5.0-compatibility

    Add ggplot 3.5.0 compatibility (guides and layout ggproto)
    thackl authored Mar 4, 2024
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  5. reduce package size by replacing .fna files with .fna.fai indices, re…

    …moving unnecessary data; updated examples;
    thackl committed Mar 4, 2024
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  7. bump version to 1.0.0

    thackl committed Mar 4, 2024
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  9. update man

    thackl committed Mar 4, 2024
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Commits on Mar 5, 2024

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  2. Merge pull request #168 from thackl/cran-ready

    Make gggenomes ready for CRAN submission
    thackl authored Mar 5, 2024
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Commits on Mar 8, 2024

  1. Fix imports for sessionInfo

    iimog committed Mar 8, 2024
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  2. Add r-hub workflow

    iimog committed Mar 8, 2024
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  3. Add pandoc setup for r-lib

    iimog committed Mar 8, 2024
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  4. Add tinytex setup for r-lib

    iimog committed Mar 8, 2024
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Commits on Mar 25, 2024

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Commits on Jun 6, 2024

  1. Re-implement read_seq_len in R

    iimog committed Jun 6, 2024
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  2. Ignore vscode dir

    iimog committed Jun 6, 2024
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  4. Re-generate man

    iimog committed Jun 6, 2024
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  5. Ignore vscode in R build

    iimog committed Jun 6, 2024
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  6. S3 generic/method consistency

    iimog committed Jun 6, 2024
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  3. Update rhub action

    iimog committed Jun 7, 2024
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  3. Compress ext gorg.gff file

    iimog committed Jun 19, 2024
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  5. Ignore pkgdown cache

    iimog committed Jun 19, 2024
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  4. Remove quote for geom

    quotes are for package names only
    iimog committed Jun 25, 2024
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  5. Fix missing \value tags in Rd files

    Instances found using checkhelper::find_missing_tags()
    Automatic formatting applied
    iimog committed Jun 25, 2024
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  6. Apply auto-formatting

    iimog committed Jun 25, 2024
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Commits on Jun 27, 2024

  1. Fix missing \value Rd-tags

    iimog committed Jun 27, 2024
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  2. Simplify expression

    iimog committed Jun 27, 2024
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Commits on Jun 28, 2024

  1. 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
    iimog authored Jun 28, 2024
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Commits on Jul 18, 2024

  1. Fix typo

    Co-authored-by: x <[email protected]>
    iimog and wagon-master committed Jul 18, 2024
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Commits on Aug 30, 2024

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  2. bump version

    thackl committed Aug 30, 2024
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