NEWS.md

In YuLab-SMU/ggmsa: Plot Multiple Sequence Alignment using 'ggplot2'

ggmsa 1.3.3

• calling \dontrun{} for examples on ggmsa()

ggmsa 1.3.2

• bugfix: geom_msaBar conservation layer incorrectly aligned issues#34(2022-5-13, Fri)

ggmsa 1.3.1

• A new feature--selects ancestral sequence on Tree-MSA plot treeMSA_plot (2022-4-14, Thu)
• A new feature--visualization of genome alignment ggmaf (2022-4-14, Thu)
• A test feature--visualization protein-protein interactive (2022-4-14, Thu)
• updated the way smooth is invoked on simplot(2022-01-03, Mon)

ggmsa 1.1.4

added smoothed curve on simplot.(2021-12-17, Fri)

ggmsa 1.1.3

fixed the typo in "posHighligthed", and changed it to snake_case "position_highlight" from camelCase "posHighligthed" (2021-12-13, Mon)

ggmsa 1.1.2

fixed the assignment error on line 155 'seqlogo.R'

ggmsa 1.1.1

fixed error: using || instead of | on 110 lines in geom_msa.R

ggmsa 0.99.0 or 0.99.x

(Prepare for submission to Bioconductor, 2021-09-22 Wed)

• 0.99.1 update DESCRIPTION and NEWS files (2021-09-28, Tue)
• 0.99.2 add documentation for row data in extdata/inst and clean up code (2021-09-29, Wed)
• 0.99.3 remove some vignettes from master (build on the gh-pages branch) (2021-10-1, Fri)
• 0.99.4 remove 'stringr' package from 'Imports' (2021-10-11, Mon)
• 0.99.5 make the consensus_views compatible ggtreeExtra and add package description. (2021-10-21, Thu)

ggmsa 0.0.10

• update default color schemes in lower part of the SeqDiff plot (2021-08-20, Fri)

ggmsa 0.0.9

• import R4RNA to fix R check (2021-08-03, Tue)

ggmsa 0.0.8

• bugfix: fix variable names error in color_scheme. (2021-07-29, Thu)
• The migration of sequence recombination functionality from seqcombo package. (2021-07-20, Tue)

ggmsa 0.0.7

• added gghelix() and geom_helix().(2021-04-1, Thu)
• added option to show the fill legend.(2021-03-23, Tue)
• added a error message to remind that "sequences must have unique names".(2021-03-18, Thu)
• added ggSeqBundle() to plot Sequence Bundles for MSAs based ggolot2 (2021-03-18, Thu)

ggmsa 0.0.6

• supports linking ggtreeExtra. (2021-01-21, Thu)
• bugfix: reversed sequence in 'tree + geom_facet(font)' . (2021-01-21, Thu)
• bugfix: partitioning error when the sequence starting point greater than 1. (2021-01-21, Thu)
• bugfix: generates continuous x-axis labels for each panel. (2021-01-21, Thu)
• supports customize colors custom_color. (2020-12-28, Mon)

ggmsa 0.0.5

• added a new view called by_conservation.(2020-12-22, Tue)
• added a new color scheme Hydrophobicity and a new parameter border.(2020-12-21, Mon)
• rewrite the function facet_msa().(2020-12-03, Thu)
• Debug: tree + geom_facet(geom_msa()) does not work.(2020-12-03, Thu)
• added a new function geom_msaBar().(2020-12-03, Thu)
• added a new parameter ignore_gaps used in consensus views.(2020-10-09, Fri)
• debug in consensus views (2020-10-05, Mon)
• added consensus views (2020-9-30, Wed)
• added new colors LETTER and CN6 provided by ShixiangWang.issues#8

ggmsa 0.0.4

• fixed warning message in msa_data.R (2020-4-26, Sun)
• added ggplot_add methods for geom_*() (2020-4-24, Fri)
• added a parameter seq_name in ggmsa() (2020-4-23, Thu)
• added a new function facet_msa() --> break down the MSA (2020-4-17, Fri)
• added a parameter posHighlighted in ggmsa() (2020-4-17, Fri)
• created a new layer geom_asterisk() to optimized geom_seed() (2020-4-11, Sta)
• added new functions available_colors(), available_fonts() and available_msa() (2020-3-30, Thu)
• added a new function geom_seed() --> highlight the seed region in miRNA sequences (2020-3-27, Fri)
• added a new function ggmotif()--> plot sequence motifs independently (2020-3-23, Tue)
• added a Monospaced Font DroidSansMono (2020-3-23, Mon)

ggmsa 0.0.3

• release of v=0.0.3 (2020-03-16, Mon)
• added a new function geom_GC() --> plot GC content in MSA (2020-02-28, Fri)
• added a new function geom_seqlogo() --> plot plot sequence motifs in MSA (2020-02-14, Fri)
• used a proportional scaling algorithm (2020-01-08, Wed)

ggmsa 0.0.2

• support plot sequence logo (2019-12-25, Wed)
• added three fonts：helvetical, times_new_roman, mono (2019-12-21, Sta)
• ~~added three fonts：serif_font, Montserrat_font, roboto_font (2019-12-17, Tue)~~
• added internal outline polygons (2019-12-15, Sun)
• bug fixed of tidy_msa
• import seqmagick for parsing fasta
• tidy_msa for converting msa file/object to tidy data frame (2019-12-09, Mon)

ggmsa 0.0.1

• initial CRAN release (2019-10-17, Thu)
• removed from CRAN on 2021-08-17

YuLab-SMU/ggmsa documentation built on Dec. 23, 2024, 7:54 p.m.