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ggalign 0.0.5

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@Yunuuuu Yunuuuu released this 15 Nov 22:12

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 plot_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 plot_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