ggtree-py 0.1.0__py3-none-any.whl

ggtree/__init__.py

@@ -0,0 +1,569 @@
+"""
+ggtree: Grammar of Graphics for Phylogenetic Trees in Python (v4.3.2)
+Complete Python port of the R/Bioconductor ggtree package.
+"""
+
+__version__ = "0.1.0"
+__r_ggtree_version__ = "4.3.2"
+
+from .dataframe import (
+    DataFrame,
+    TblTree,
+    ColumnSeries,
+    Factor,
+    options,
+    getOption,
+    attr,
+    set_attr,
+    data_frame,
+    tibble,
+    c,
+    rep,
+    seq,
+    seq_len,
+    seq_along,
+    paste,
+    paste0,
+    factor,
+    rnorm,
+    runif,
+    rbinom,
+    sample,
+    set_seed,
+    LETTERS,
+    letters,
+    NA,
+    TRUE,
+    FALSE,
+    NULL,
+    is_na,
+    match,
+    mutate,
+    filter,
+    select,
+    arrange,
+    left_join,
+    full_join,
+    inner_join,
+    bind_rows,
+    unnest,
+    read_table,
+    read_csv,
+)
+
+from .tree import (
+    Phylo,
+    TreeData,
+    MultiPhylo,
+    TreeDataList,
+    Hclust,
+    hclust,
+    read_tree,
+    read_beast,
+    read_nhx,
+    read_jplace,
+    read_fasta,
+    write_tree,
+    rtree,
+    rmtree,
+    stree,
+    estimate_dates,
+    reorder_phylo,
+    ladderize,
+    di2multi,
+    as_polytomy,
+    extract_clade,
+    Ntip,
+    Nnode,
+    Nnode2,
+    getNodeNum,
+    is_rooted,
+    get_tree,
+    as_phylo,
+    as_treedata,
+    as_tibble,
+    system_file,
+    get_seqs,
+    subtrees,
+)
+
+from .tidytree import (
+    taxa2node,
+    nodeid,
+    nodelab,
+    rootnode,
+    getRoot,
+    isTip as _tidytree_isTip,
+    itself,
+    child,
+    parent as _tidytree_parent,
+    sibling,
+    ancestor,
+    offspring,
+    offspring_bulk,
+    MRCA,
+    groupOTU,
+    groupClade,
+    tree_subset,
+    td_filter,
+    td_mutate,
+    td_unnest,
+)
+
+from .layout import (
+    Date2decimal,
+    decimal2Date,
+    getXcoord2,
+    getXcoord,
+    getXcoord_no_length,
+    getXcoord_no_length_slanted,
+    getYcoord_no_length_slanted,
+    getYcoord,
+    getYcoord_tidy,
+    re_assign_ycoord_df,
+    reassign_y_from_node_to_root,
+    calculate_branch_mid,
+    calculate_angle,
+    add_angle_slanted,
+    set_branch_length_cladogram,
+    getNodes_by_postorder,
+    getNodesBreadthFirst_df,
+    layoutEqualAngle,
+    applyLayoutDaylight,
+    layoutDaylight,
+    layoutApe,
+    layoutTreeAndLeaf,
+    scaleX_by_time_from_mrsd,
+    scaleY,
+    adjust_hclust_tip_edge_len,
+    tree_layout,
+    fortify,
+    get_layout,
+    tip_y_alignment,
+    check_reverse,
+    get_clade_position_,
+    get_clade_position,
+    clade_geometry,
+    adjust_cladelabel_angle,
+)
+
+from .aes import (
+    SymExpr,
+    CallableSymExpr,
+    Aes,
+    aes,
+    modifyList,
+    eval_expr,
+    eval_subset,
+    node,
+    label,
+    branch,
+    branch_length,
+    x,
+    y,
+    angle,
+    group,
+    rate,
+    posterior,
+    height,
+    value,
+    id,
+    _id,
+    place,
+    type_,
+    annote,
+    image,
+    offset,
+    ta1,
+    ta2,
+    taxa1,
+    taxa2,
+    tree,
+    v,
+    S,
+    trait,
+    score,
+)
+
+isTip = CallableSymExpr("isTip", _tidytree_isTip)
+parent = CallableSymExpr("parent", _tidytree_parent)
+
+from .themes_scales import (
+    PlotModifier,
+    Theme,
+    Scale,
+    Coord,
+    rel,
+    unit,
+    margin,
+    arrow,
+    element_blank,
+    element_text,
+    element_line,
+    element_rect,
+    guide_legend,
+    guide_colorbar,
+    guides,
+    theme,
+    theme_tree,
+    theme_tree2,
+    theme_dendrogram,
+    theme_inset,
+    theme_bw,
+    theme_minimal,
+    theme_void,
+    theme_classic,
+    labs,
+    ggtitle,
+    xlab,
+    ylab,
+    xlim,
+    ylim,
+    xlim_expand,
+    xlim_tree,
+    hexpand,
+    vexpand,
+    ggexpand,
+    revts,
+    scale_x_range,
+    coord_cartesian,
+    coord_flip,
+    coord_polar,
+    coord_fixed,
+    facet_wrap,
+    facet_grid,
+    new_scale_fill,
+    new_scale_color,
+    new_scale_colour,
+    scale_color_manual,
+    scale_colour_manual,
+    scale_fill_manual,
+    scale_color_continuous,
+    scale_colour_continuous,
+    scale_fill_continuous,
+    scale_color_gradient,
+    scale_colour_gradient,
+    scale_fill_gradient,
+    scale_color_gradient2,
+    scale_fill_gradient2,
+    scale_color_viridis_c,
+    scale_colour_viridis_c,
+    scale_fill_viridis_c,
+    scale_color_viridis_d,
+    scale_colour_viridis_d,
+    scale_fill_viridis_d,
+    scale_color_brewer,
+    scale_fill_brewer,
+    scale_x_continuous,
+    scale_y_continuous,
+    scale_x_date,
+    scale_x_ggtree,
+    scale_size,
+    scale_size_continuous,
+    scale_alpha,
+    scale_shape_manual,
+    scale_linetype_manual,
+    scale_color,
+    add_colorbar,
+    set_hilight_legend,
+)
+
+from .geoms import (
+    Layer,
+    LayerList,
+    geom_tree,
+    geom_tree2,
+    stat_tree,
+    geom_tiplab,
+    geom_tiplab2,
+    geom_nodelab,
+    geom_nodelab2,
+    geom_point2,
+    geom_point,
+    geom_tippoint,
+    geom_nodepoint,
+    geom_rootpoint,
+    geom_text2,
+    geom_text,
+    geom_label2,
+    geom_label,
+    geom_segment2,
+    geom_segment,
+    geom_aline,
+    geom_hilight,
+    geom_highlight,
+    geom_hilight_encircle,
+    geom_cladelab,
+    geom_cladelabel,
+    geom_cladelabel2,
+    geom_strip,
+    geom_striplab,
+    geom_taxalink,
+    geom_tanglelink,
+    geom_treescale,
+    geom_balance,
+    geom_range,
+    geom_rootedge,
+    geom_zoom_clade,
+    geom_motif,
+    geom_inset,
+    geom_bar,
+    geom_col,
+    geom_tile,
+    geom_raster,
+    geom_line,
+    geom_path,
+    geom_area,
+    geom_ribbon,
+    geom_rect,
+    geom_polygon,
+    geom_curve,
+    geom_vline,
+    geom_hline,
+    geom_abline,
+    geom_boxplot,
+    geom_violin,
+    geom_density,
+    geom_histogram,
+    geom_errorbar,
+    geom_errorbarh,
+    geom_linerange,
+    geom_pointrange,
+    geom_tree_interactive,
+    geom_point_interactive,
+    geom_tiplab_interactive,
+    geom_tiplab2_interactive,
+    geom_nodelab_interactive,
+    geom_nodelab2_interactive,
+    geom_cladelab_interactive,
+    geom_cladelabel_interactive,
+    geom_hilight_interactive,
+    geom_strip_interactive,
+    geom_taxalink_interactive,
+    geom_label2_interactive,
+    geom_point2_interactive,
+    geom_segment2_interactive,
+    geom_text2_interactive,
+    GeomHilightEncircle,
+    GeomInteractiveCurvelink,
+    GeomInteractiveHilightEncircle,
+    GeomInteractiveHilightRect,
+    GeomInteractiveLabelGGtree,
+    GeomInteractivePointGGtree,
+    GeomInteractiveSegmentGGtree,
+    GeomInteractiveTextGGtree,
+    StatBalance,
+    ggtree_set_interactive,
+    ggtree_unset_interactive,
+)
+
+from .manipulate import (
+    get_taxa_name,
+    viewClade,
+    zoomClade,
+    collapse,
+    expand,
+    rotate,
+    flip,
+    scaleClade,
+    open_tree,
+    rotate_tree,
+    layout_ggtree,
+    layout_rectangular,
+    layout_circular,
+    layout_fan,
+    layout_inward_circular,
+    layout_dendrogram,
+    label_pad,
+    range_format,
+    reroot,
+    rescale_tree,
+    gzoom,
+    identify,
+    scale_color_subtree,
+    scale_colour_subtree,
+)
+
+from .compose import (
+    gheatmap,
+    get_heatmap_column_position,
+    msaplot,
+    geom_facet,
+    facet_plot,
+    facet_data,
+    facet_labeller,
+    facet_widths,
+    nodebar,
+    nodepie,
+    inset,
+    ggdensitree,
+    Tanglegram,
+    as_tanglegram,
+    as_tanglegram_cophylo,
+    as_tanglegram_default,
+    as_tanglegram_tanglegram,
+    ggdoubletree,
+    PlotList,
+    multiplot,
+    plot_list,
+)
+
+from .plot import (
+    GGTree,
+    BuiltPlot,
+    BuiltLayout,
+    ggplot,
+    ggtree,
+    ggplot_build,
+    is_ggplot,
+    ggsave,
+    last_plot,
+)
+
+
+# ---------------------------------------------------------------------------
+# R-namespace dot-Call Compatibility Proxies
+# Allows R-style expressions in Python:
+#   read.tree(...), read.beast(...), system.file(...), data.frame(...),
+#   set.seed(...), as.polytomy(...), ape.rtree(...), ggplot2.ggplot_build(...)
+# ---------------------------------------------------------------------------
+
+class _ReadNamespace:
+    tree = staticmethod(read_tree)
+    beast = staticmethod(read_beast)
+    nhx = staticmethod(read_nhx)
+    jplace = staticmethod(read_jplace)
+    fasta = staticmethod(read_fasta)
+    table = staticmethod(read_table)
+    csv = staticmethod(read_csv)
+
+
+class _WriteNamespace:
+    tree = staticmethod(write_tree)
+
+
+class _SystemNamespace:
+    file = staticmethod(system_file)
+
+
+class _DataNamespace:
+    frame = staticmethod(data_frame)
+
+
+class _SetNamespace:
+    seed = staticmethod(set_seed)
+
+
+class _AsNamespace:
+    polytomy = staticmethod(as_polytomy)
+    phylo = staticmethod(as_phylo)
+    treedata = staticmethod(as_treedata)
+    tibble = staticmethod(as_tibble)
+    tanglegram = staticmethod(as_tanglegram)
+
+
+class _IsNamespace:
+    na = staticmethod(is_na)
+    ggplot = staticmethod(is_ggplot)
+    rooted = staticmethod(is_rooted)
+
+
+class _ApeNamespace:
+    rtree = staticmethod(rtree)
+    rmtree = staticmethod(rmtree)
+    stree = staticmethod(stree)
+    read_tree = staticmethod(read_tree)
+    write_tree = staticmethod(write_tree)
+    read = _ReadNamespace()
+    write = _WriteNamespace()
+    Ntip = staticmethod(Ntip)
+    Nnode = staticmethod(Nnode)
+    di2multi = staticmethod(di2multi)
+    ladderize = staticmethod(ladderize)
+    extract_clade = staticmethod(extract_clade)
+    estimate_dates = staticmethod(estimate_dates)
+    is_rooted = staticmethod(is_rooted)
+    subtrees = staticmethod(subtrees)
+
+
+class _TreeioNamespace:
+    read_tree = staticmethod(read_tree)
+    read_beast = staticmethod(read_beast)
+    read_nhx = staticmethod(read_nhx)
+    read_jplace = staticmethod(read_jplace)
+    read_fasta = staticmethod(read_fasta)
+    read = _ReadNamespace()
+    get_tree = staticmethod(get_tree)
+    get_seqs = staticmethod(get_seqs)
+    Nnode = staticmethod(Nnode)
+    Nnode2 = staticmethod(Nnode2)
+    Ntip = staticmethod(Ntip)
+    as_phylo = staticmethod(as_phylo)
+    as_treedata = staticmethod(as_treedata)
+    rescale_tree = staticmethod(rescale_tree)
+
+
+class _TidytreeNamespace:
+    nodeid = staticmethod(nodeid)
+    nodelab = staticmethod(nodelab)
+    rootnode = staticmethod(rootnode)
+    isTip = staticmethod(_tidytree_isTip)
+    child = staticmethod(child)
+    parent = staticmethod(_tidytree_parent)
+    sibling = staticmethod(sibling)
+    ancestor = staticmethod(ancestor)
+    offspring = staticmethod(offspring)
+    MRCA = staticmethod(MRCA)
+    groupOTU = staticmethod(groupOTU)
+    groupClade = staticmethod(groupClade)
+    tree_subset = staticmethod(tree_subset)
+    as_tibble = staticmethod(as_tibble)
+    as_treedata = staticmethod(as_treedata)
+    as_phylo = staticmethod(as_phylo)
+
+
+class _Ggplot2Namespace:
+    ggplot = staticmethod(ggplot)
+    aes = staticmethod(aes)
+    ggplot_build = staticmethod(ggplot_build)
+    is_ggplot = staticmethod(is_ggplot)
+    ggsave = staticmethod(ggsave)
+    rel = staticmethod(rel)
+    unit = staticmethod(unit)
+    margin = staticmethod(margin)
+    arrow = staticmethod(arrow)
+    element_blank = staticmethod(element_blank)
+    element_text = staticmethod(element_text)
+    element_line = staticmethod(element_line)
+    element_rect = staticmethod(element_rect)
+    theme = staticmethod(theme)
+    theme_bw = staticmethod(theme_bw)
+    theme_minimal = staticmethod(theme_minimal)
+    theme_void = staticmethod(theme_void)
+    theme_classic = staticmethod(theme_classic)
+    labs = staticmethod(labs)
+    ggtitle = staticmethod(ggtitle)
+    xlab = staticmethod(xlab)
+    ylab = staticmethod(ylab)
+    xlim = staticmethod(xlim)
+    ylim = staticmethod(ylim)
+    coord_cartesian = staticmethod(coord_cartesian)
+    coord_flip = staticmethod(coord_flip)
+    coord_polar = staticmethod(coord_polar)
+    coord_fixed = staticmethod(coord_fixed)
+    facet_wrap = staticmethod(facet_wrap)
+    facet_grid = staticmethod(facet_grid)
+    fortify = staticmethod(fortify)
+
+
+read = _ReadNamespace()
+write = _WriteNamespace()
+system = _SystemNamespace()
+data = _DataNamespace()
+set_ = _SetNamespace()
+as_ = _AsNamespace()
+is_ = _IsNamespace()
+ape = _ApeNamespace()
+treeio = _TreeioNamespace()
+tidytree = _TidytreeNamespace()
+ggplot2 = _Ggplot2Namespace()