Skip to content

NEWS.md

Latest commit

 

History

History
355 lines (186 loc) · 13.8 KB

NEWS.md

File metadata and controls

355 lines (186 loc) · 13.8 KB
Raw

ggalign (development version)

ggalign 1.2.0

  • Fixed alignment of absolute panel dimensions when using theme(panel.widths, panel.heights) in ggplot2 v4.0.0.

  • 'alignpatch-*' scripts have been fully refactored with S7 classes, with more informative and consistent naming.

  • Improved align_plots() to properly handle strips with different placements.

  • Renamed the original alignpatch() to patch() for clearer and more consistent naming.

  • The Patch object is now exported for external use.

  • Refactored patch_titles to the new S7-based patch_title class (soft-deprecated the old version).

  • Renamed the original patch() to as_grob() for clearer.

ggalign 1.1.0

The internal structure has been fully refactored, with more informative and consistent naming.

  • remove element_polygon()/element_curve(), to be implemented upstream in ggplot2

  • new layout_theme() to control layout theming.

  • Deprecated the theme argument in layout_annotation().

  • Migrated all internal objects to the S7 class system.

  • replace with_quad() with quad_scope() and deprecate old name.

  • new layout_tags(): add support for tagging plots and nested layouts.

  • & operator now can work for align_plots().

  • new geom_magick() object to draw images as point shapes using magick

  • The sector_spacing argument in facet_sector() can be a multi-value numeric (#73)

  • new argument split in align_phylo() to support splitting phylo objects into multiple trees (#74)

  • The fortify_matrix() method for phylo object is removed

  • new plot_ideogram() function to add an aligned cytoband ideogram plot

ggalign 1.0.2

  • align_plots(): Always ensure that plots placed in a border collect their guides, if any guides are to be collected in that border. This prevents overlap, unless the guides will be collected by the parent layout.

  • new scale for z aesthetic: scale_z_continuous, scale_z_binned, scale_z_discrete, scale_z_ordinal, scale_z_datetime, scale_z_date

  • geom_subrect() and geom_subtile() gain nrow and ncol arguments to control the layout, and deprecate direction argument

  • ggoncoplot() gains a new argument remove_duplicates to control whether to remove duplicated variants within the same cell.

  • fortify_data_frame.matrix() gains a new argument lvls, allowing matrix values to be converted into a factor.

  • circle_layout(): fix wrong sector_spacing due to the operator precedence when building.

  • circle_layout(): rename spacing_theta argument to sector_spacing argument, and deprecate spacing_theta argument.

  • circle_continous: gains spacing_theta argument to control the sector spacing for all plots.

  • facet_sector(): deprecate radial argument, user should add the coord_radial() or coord_circle() directly to the plot.

  • new magickGrob() to construct grob with magick processing.

ggalign 1.0.1

  • fix R CMD check error for the updated version of ggplot2 3.5.2.

  • new grob channelGrob() used to create grobs across different facet.

  • fix patch.gList method.

ggalign 1.0.0

This is a major release. While not many new features have been added, this marks the first release where the entire layout system has been completed.

Breaking changes

  • align_reorder() has been renamed to align_order2().

  • geom_draw2() has been renamed to geom_gshape().

New features

  • Now circle_layout() support multiple facets.

  • new facet_sector() function to add Facet support for polar coordinates

  • new coord_circle() function to provide additional customization options for coord_radial()

  • new tune() method shape ("oncoplot") for matrix

ggalign 0.1.0

Breaking changes

  • Now, all *_free() layouts have been removed, all layout has been splitted into two type: align discrete or continous vairables.

New features

  • new helper function memo_order() to reorder the oncoplot samples.

  • new geom_subrect() and geom_subtile() to subdivide rectangles with shared borders into a grid.

  • new cross_link function to reset the layout ordering index or layout panel group, and add plot to connect selected observations.

  • new cross_mark function to reset the layout ordering index or layout panel group, and add plot to annotate observations.

  • new pair_links() function to create pairs of observation groups.

  • new mark_draw(), mark_line(), mark_tetragon() to define the links to connect the marked observations.

  • new link_draw(), link_line(), link_tetragon() to define the links to connect a pair of observations

  • new ggmark() to add a plot to annotate selected observations.

  • new element_vec() functions to apply function to the vectorized fields of the theme element object.

  • new no_expansion() function to remove scale expansion.

  • new layout circle_layout() to arrange plot in a circular.

  • new raster_magick() function to post-processing the image raster with magick package was added.

  • new fortify_matrix.GISTIC() method for GISTIC object from maftools package (#24).

  • + operator now will respect with_quad().

  • new ggalign_attr_set() and ggalign_attr_get() for basic operations of attached attribute.

  • new geom_draw() function to draw ggplot2 layer with customized draw function.

Bug fixes

  • fix breaks and labels not work well in discrete scale (#30, #32)

  • fix wrong results of fortify_matrix.MAF() method

Improvements

  • Now, with_quad() wraps the object into a list with the class with_quad. This approach offers greater flexibility in defining the actions associated with with_quad, allowing for more customizable behavior (#26, @Yunuuuu).

  • Now, we always set as.table = FALSE when using ggplot2 facet_*() functions, we don't need to reorder the panel when drawing.

  • free_gg, align and the new cross_link objects have been collapsed to one class ggalign_plot

ggalign 0.0.5

Breaking changes

  • direction argument in stack_layout()/ggstack() is soft-deprecated now, user must provide it manually.

  • set_context, order, and name arguments in align_*() and ggheatmap() are soft-deprecated, which is advised to use active argument.

  • guides, free_guides, free_spaces, free_labs, and plot_data arguments in align_*() and ggheatmap() are deprecated, which is advised to use scheme_align function instead.

  • theme argument in align_*() and ggheatmap() is deprecated, which is advised to use plot_theme function.

  • what argument in stack_active() is soft-deprecated, user is advised to use stack_switch() to change the active plot with what.

  • align_panel()/ggpanel() is deprecated, user is advised to use ggalign(data = NULL) instead.

New features

  • new quad_layout() to create layout allowing free from alignment.

  • new quad_alignv(), quad_alignh(), quad_free()/ggside(), quad_alignb() alias for quad_layout().

  • stack_layout() now gains a type argument to control whether the layout should align observations.

  • new ggoncoplot() function to draw oncoprint.

  • new ggfree() function to add ggplot to the layout.

  • new fortify_matrix() function to convert any objects to a matrix, and add fortify_matrix() method for MAF object.

  • new fortify_data_frame() function to convert any objects to a data frame.

  • now, a special attribute ggalign can be used to pass additional informations across the building process, and a new function ggalign_attr() can be used to extract the data from the attribute.

  • new plot_theme() function to control the default theme of the plot in layout.

  • new plot_data() function to control the data transformation of the plot in layout.

  • new scheme_align() function to control specifications of the plot in layout.

  • new with_quad() function to control the - operator context.

  • new quad_init() function to initialize the annotation with self-provided data.

  • new stack_switch() and quad_switch() to switch active plots for stack_layout() and quad_layout().

  • new anno_top(), anno_left(), anno_bottom() and anno_right() alias for add annotation in quad_layout().

  • align_dendro() gain a new argument cutree to customize the process of tree cutting.

  • reorder_dendrogram argument in align_dendro() function now can accept a function to reorder the tree.

  • new layer_order() function to change the ggplot2 layer adding order.

  • new theme_no_axes() function to remove axis elements.

  • new geom_pie() function to draw pie charts.

Bug fixes

  • fix bug when apply free_border in alignpatches object.

  • fix bug when provide a function in distance argument of align_dendro()

  • fix bug when provide hclust or dendrogram in method argument of align_dendro()

  • fix bug of coord_ggalign() for discrete scale

Improvements

  • merge function has been implemented with vctrs for performance

  • for large matrix (> 20000 cells), automatically use geom_raster()

  • {data.table} is now removed from the dependency

ggalign 0.0.4

  • layout_heatmap()/ggheatmap() arguments width/height have been renamed .width/.height to helps avoid conflicts with arguments from geom_tile().

  • the nestet alignpatches theme by default will inherit from the parent alignpatches

  • new layout_title() function, now layout_annotation() only control the layout theme

  • add ggrastr::rasterize method for both ggheatmap() and ggstack()

  • set_context argument in align_dendro() now depends on plot_dendrogram by default

  • align_dendro() gain a new argument reorder_dendrogram to control whether to reorder the generated dendrogram based on the mean values.

  • align_order2() now splitted into two function align_order() and align_order2()

  • dendrogram_data() gain a new argument reorder_branches to control whether to reorder the input leaf_braches based on the tree.

  • align_dendro() gain new argument merge_dendrogram to control whether the dendrograms in multiple groups should be merged

  • dendrogram height axis will be automatically reversed in bottom and left annotation stack

  • heatmap fill color scale now default use scale_fill_gradient2(low = "blue", high = "red") for continuous values.

  • Coord is used to set limits instead of Scale

  • all free_* arguments now accept the same argument of the corresponding free_* functions.

  • new theme_ggalign() function for the default theme of ggalign package

  • export option ggalign.default_theme allow user to change the global default theme

  • new free_guide() function, to override the layout guides argument for single plot

  • geom_draw() now utilize patch() function to convert objects into grob

  • internal changes: all vectors have been operated with vctrs package

  • stack_layout(): gain sizes argument to control the relative sizes of the stack

  • align_()*: now order argument only control the plot area.

  • align_order2() now can accept an ordering character names.

  • export order2() function

  • align_order2(): fun argument has been renamed to order argument, and it can now accept the ordering integer index directly

  • fun in align_order2() now can return any statistics which can be handled by order2()

  • fix ggheatmap() order not work when put in a stack layout

  • method in hclust2() can now return any objects which can be coerced into hclust, or you can provide such object directly in method.

  • hclust2() now can accept distance = NULL

  • hmanno(), stack_active(), and align_*() functions gain a new argument theme to control the theme for the plot.

  • new layout_annotation() and layout_theme() to modify the layout components

  • borders argument in free_space() has been renamed to spaces

  • {tibble} is now removed from the dependency

  • align_plots() now can accept gList, function, recordedplot, trellis, pheatmap, Heatmap, HeatmapAnnotation, and HeatmapList, we have added alignpatch method for these objects.

  • add patch method for gList, function, recordedplot, trellis, pheatmap, Heatmap, HeatmapAnnotation, and HeatmapList

  • fix a bug in wrap() function where duplicated names in gtable cause some grobs missing

  • new free_vp() function to customize the viewport when aligning.

  • StackLayout and HeatmapLayout methods have been collapsed into one method for Layout class

  • New Patch class, now we can extend the alignment process of any object and customize the building process with ggproto.

  • fix missing variable labs in the free_space method of PatchAlignpatches

ggalign 0.0.3

  • Add package logo

  • new inset() function

  • add package quotes in DESCRIPTION

  • add return value docs for exported function or methods

ggalign 0.0.2

  • omit the redudnant description and add single quote for package name

ggalign 0.0.1

Features

ggalign pacakge provides two layout to arrange ggplot objects:

  • heatmap_layout()/ggheatmap(): Arrange ggplot into a Heatmap layout. See vignette("heatmap-layout") for details.

  • stack_layout()/ggstack(): Arrange ggplot vertically or horizontally. See vignette("stack-layout") for details.

To further customize these layouts, we offer following functions:

  • align_group(): Group layout axis into panel with a group variable.
  • align_kmeans(): Group layout axis into panel by kmeans
  • align_order2(): Reorders layout observations based on weights or summary statistics.
  • align_dendro(): Reorder or Group layout based on hierarchical clustering

For more detailed instructions on customizing layouts, see the vignette: vignette("layout-customize").

Additionally, plots can be added in the layout with following functions:

  • align_gg()/ggalign(): Create ggplot object with a customized data.
  • align_panel()/ggpanel(): Create ggplot object with the layout panel data.

For more information on adding plots, refer to the vignette: vignette("layout-plot").