glydraw 0.6.3
glydraw 0.6.2
Minor improvements and bug
fixes
- Fix nested Fuc-like side-chain layout so xyloglucan-like branches
preserve residue order and linkage annotations. (#51)
glydraw 0.6.1
Minor improvements and bug
fixes
- Fix Fuc-like triangle geometry so triangle bases and apexes align
with rectangle node bounds. (#49, #50)
glydraw 0.6.0
Breaking changes
export_cartoons() no longer supports
glyexp::experiment() input, and glyexp is no
longer a package dependency. (#33)- Specifying optional arguments in a positional manner is no longer
supported. Please use
arg = value instead. (#40)
New features
- Add the
colors parameter to draw_cartoon()
and export_cartoons() for customizing monosaccharide fill
colors. (#44)
- Add the
fuc_orient parameter to
draw_cartoon() and export_cartoons() for
choosing whether Fuc triangles always point upward or flex toward their
linkage direction. (#42)
- Add the
scale parameter to save_cartoon()
and export_cartoons() for changing output pixel dimensions
while preserving cartoon appearance. (#35)
- Add the
node_size parameter to
draw_cartoon() and export_cartoons() for
scaling residue cartoon sizes. Values larger than 2 are
rejected because residues overlap. (#36)
- Add the
edge_linewidth and node_linewidth
parameters to draw_cartoon() and
export_cartoons() for customizing linkage line and node
border widths. (#34)
- Add the
red_end parameter to
draw_cartoon() and export_cartoons() for
custom reducing-end text or a wavy reducing-end annotation. (#31)
Minor improvements and bug
fixes
- Fix substituent label alignment so horizontal labels are
bottom-aligned and vertical labels are left-aligned. (#48)
- Extend Fuc-style branch layout and flexible orientation to
additional Fuc-like residues. (#46)
- Fix
draw_cartoon() for structures with two core Fuc
branches and one b1-4 GlcNAc branch, avoiding an igraph vertex-selection
error and keeping the b1-4 GlcNAc aligned with the core GlcNAc.
(#45)
- Deprecate
dpi for save_cartoon() and
export_cartoons() because glydraw uses an internal fixed
design scale. Supplying dpi now warns that the argument is
ignored. (#35)
- Keep substituent annotations visible when
show_linkage = FALSE. (#41)
- Fix diagonal HexNAc linkage annotation offsets when
orient = "V". (#43)
- Adjust linkage annotation offsets for diagonal HexNAc links.
(#29)
glydraw 0.5.1
Minor improvements and bug
fixes
- Use SNFG standard colors. (8573759)
- Minor aesthetic adjustments to line width and node size. (427e8d0,
4466f88)
glydraw 0.5.0
New features
- Use native ggplot2 theme to manage cartoon size, so
ggview is no longer dependent. (#27)
Minor improvements and bug
fixes
- Fix overlapping linkage annotations for some glycans. (#21)
- Fix overlapping a1-3 and a1-6 core Fucose residues. (#23)
- Orient reducing end annotation line vertically when
orient = "V". (#24)
- Redesign the node coordination layout algorithm to fix inaccurate
branch spacing for some glycans. (#26, #28)
glydraw 0.4.1
Minor improvements and bug
fixes
- Fix substituent annotations in glycan cartoons. (#16)
- Fix reducing-end Fuc orientation in O-Fuc glycans. (#15)
- Make
export_cartoons() create the output directory when
needed. (#17)
- Make
export_cartoons() use vector names as output
filenames when available. (#17)
glydraw 0.4.0
Breaking changes
- Remove the
mono_size parameter of
draw_cartoon(). (9b05e6c)
New features
- Add a
highlight parameter to
draw_cartoon(). (7e57a54, 3745ec8, c1057ba)
- Add
export_cartoons() to save multiple glycan structure
cartoons to files. (e1ac3c3)
Minor improvements and bug
fixes
- Fix the bug that reducing end annotation was not shown with unknown
anomer information. (#12)
- Fix the bug that glycans with only one monosaccharide could not be
plotted. (#11)
- Fix the bug that “?” in linkages was not correctly handled.
(#9)
- Fix the incorrect reducing end annotation direction in some
situations. (#8)
- Fix the bug that glycan structures with multiple branches had
incorrect layouts. (2ac4e9f)
- Fix the bug that “png” is not supported in
save_cartoon(). (fed89b9)
- Fix the bug that structures with generic “NeuAc” and “NeuGc” cannot
be plotted. (3b78303)
glydraw 0.3.1
Minor improvements and bug
fixes
- Update dependency to glyrepr 0.10.0.
- Fix various bugs including illegal character processing, fucose
arrangement, and display sizing issues.
glydraw 0.3.0
Breaking changes
- Remove the
border_px and path parameters
from save_cartoon().
Minor improvements and bug
fixes
- Now we use
ggview instead of ggimage for
size fixing, which relies on rstudioapi::viewer() to
display the plot. You might feel some difference in the display effect,
but the SNFG itself keeps the same.
glydraw 0.2.0
Breaking changes
- Signature of
draw_cartoon() is changed into
draw_cartoon(structure, mono_size = 0.2, show_linkage = TRUE, orient = "H", ...)
for better semantics.
New features
draw_cartoon() now prints fixed-size cartoon (sizes are
calculated based on glycan structures) to the plot panel, to provide a
unified behavior with save_cartoon().- Add reducing end annotation to the cartoons (including a short
segment and the anomer of the reducing end residue).
Minor improvements and bug
fixes
- Update default aesthetic settings:
- Make residue size larger.
- Adjust linkage annotation positions.
- Add a border to the plot panel.
- Fix the issue that some linkage annotations are truncated.
- Fix the bug that glycans with only one residue cannot be plotted by
draw_cartoon().
- Fix the bug that
path parameter is mandatory in
save_cartoon(). Now it is optional, to be in line with
ggplot2::ggsave().
- Update documentation of
save_cartoon() to differentiate
it with ggplot2::ggsave().
glydraw 0.1.0