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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

First GitHub release.

These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.