glydraw 0.7.0

This version of glydraw introduced some ggplot2 extensions.

New features

• New glydraw_style() stores reusable glycan rendering options for standalone cartoons, grobs, export, ggplot2 layers, guides, and glycan scales. Explicit rendering arguments override the style. (#55)
• New geom_glycan() draws glycan cartoons for individual observations in ggplot2 plots, with support for size, rotation, justification, and cartoon appearance.
• New geom_node_glycan() draws glycan cartoons as nodes in ggraph network plots, with automatic node positioning and filtering support. (#61)
• New guide_glycan() displays glycan cartoons in ggplot2 legends.
• New scale_x_glycan() and scale_y_glycan() display glycan cartoons as discrete ggplot2 axis labels.
• New hjust_red_end() and vjust_red_end() anchor vertical and horizontal cartoons at their reducing ends in geom_glycan(), scale_x_glycan(), scale_y_glycan(), and guide_glycan(). guide_glycan() also gains hjust and vjust parameters. Reducing-end justification is the default for scale and guide cartoons along the axis perpendicular to their drawing orientation; geom_glycan() remains centered by default. (#54)

Minor improvements and bug fixes

• draw_cartoon() now places double core Fuc branches on opposite sides of the core GlcNAc when linkage positions are unavailable, keeping both connections visible. (#59, #60)
• Recognize bisecting GlcNAc from N-glycan topology when linkage information is unavailable, keeping it centered between the two mannose arms. (#58)
• draw_cartoon() now treats generic dHex residues as Fuc-like branches, using the same layout and fuc_orient behavior as Fuc. (#56)

glydraw 0.6.3

• First release on CRAN.

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.