NEWS

ggmsa 1.3.3

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

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)

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

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

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

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

(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)

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

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)

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)

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)

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

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)

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)

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)