diff options
Diffstat (limited to 'gn3')
| -rw-r--r-- | gn3/heatmaps.py | 91 |
1 files changed, 52 insertions, 39 deletions
diff --git a/gn3/heatmaps.py b/gn3/heatmaps.py index 7e7113d..ff65652 100644 --- a/gn3/heatmaps.py +++ b/gn3/heatmaps.py @@ -168,7 +168,9 @@ def get_loci_names( __get_trait_loci, [v[1] for v in organised.items()], {}) return tuple(loci_dict[_chr] for _chr in chromosome_names) -def build_heatmap(traits_names: Sequence[str], conn: Any) -> go.Figure: +def build_heatmap( + traits_names: Sequence[str], conn: Any, + vertical: bool = False) -> go.Figure: """ heatmap function @@ -234,6 +236,7 @@ def build_heatmap(traits_names: Sequence[str], conn: Any) -> go.Figure: ordered_traits_names[traits_ids[order]] for order in traits_order) }, + vertical=vertical, loci_names=get_loci_names(organised, chromosome_names)) def compute_traits_order(slink_data, neworder: tuple = tuple()): @@ -357,6 +360,7 @@ def clustered_heatmap( x_axis,#: Dict[Union[str, int], Union[str, Sequence[str]]], y_axis: Dict[str, Union[str, Sequence[str]]], loci_names: Sequence[Sequence[str]] = tuple(), + vertical: bool = False, colorscale: Sequence[Sequence[Union[float, str]]] = ( (0.0, '#0000FF'), (0.5, '#00FF00'), (1.0, '#FF0000'))) -> go.Figure: """ @@ -366,57 +370,66 @@ def clustered_heatmap( # pylint: disable=[R0913, R0914] x_axis_data = x_axis["data"] y_axis_data = y_axis["data"] - num_cols = 1 + len(x_axis_data) + num_plots = 1 + len(x_axis_data) fig = make_subplots( - rows=1, - cols=num_cols, - shared_yaxes="rows", + rows=num_plots if vertical else 1, + cols=1 if vertical else num_plots, + shared_xaxes = "columns" if vertical else False, + shared_yaxes = False if vertical else "rows", + vertical_spacing=0.010, horizontal_spacing=0.001, - subplot_titles=[x_axis["label"]] + x_axis_data, + subplot_titles=["" if vertical else x_axis["label"]] + [ + "Chromosome: {}".format(chromo) if vertical else chromo + for chromo in x_axis_data],#+ x_axis_data, figure=ff.create_dendrogram( - np.array(clustering_data), orientation="right", labels=y_axis_data)) + np.array(clustering_data), + orientation="bottom" if vertical else "right", + labels=y_axis_data)) hms = [go.Heatmap( name=chromo, - x=loci, - y=y_axis_data, + x=y_axis_data if vertical else loci, + y=loci if vertical else y_axis_data, z=data_array, + transpose=vertical, showscale=False) for chromo, data_array, loci in zip(x_axis_data, data, loci_names)] for i, heatmap in enumerate(hms): - fig.add_trace(heatmap, row=1, col=(i + 2)) - - fig.update_layout( - { - "width": 1500, - "height": 800, - "xaxis": { + fig.add_trace( + heatmap, + row=((i + 2) if vertical else 1), + col=(1 if vertical else (i + 2))) + + axes_layouts = { + "{axis}axis{count}".format( + axis=("y" if vertical else "x"), + count=(i+1 if i > 0 else "")): { "mirror": False, - "showgrid": True, - "title": "Distance" - }, - "yaxis": { - "title": y_axis["label"] - } - }) - - x_axes_layouts = { - "xaxis{}".format(i+1 if i > 0 else ""): { - "mirror": False, - "showticklabels": i == 0, - "ticks": "outside" if i == 0 else "" + "showticklabels": i == 0, + "ticks": "outside" if i == 0 else "" } - for i in range(num_cols)} + for i in range(num_plots)} - fig.update_layout( - { - "width": 4000, - "height": 800, - "yaxis": { - "mirror": False, - "ticks": "" - }, - **x_axes_layouts}) + print("vertical?: {} ==> {}".format("T" if vertical else "F", axes_layouts)) + + fig.update_layout({ + "width": 800 if vertical else 4000, + "height": 4000 if vertical else 800, + "{}axis".format("x" if vertical else "y"): { + "mirror": False, + "ticks": "", + "side": "top" if vertical else "left", + "title": y_axis["label"], + "tickangle": 90 if vertical else 0, + "ticklabelposition": "outside top" if vertical else "outside left" + }, + "{}axis".format("y" if vertical else "x"): { + "mirror": False, + "showgrid": True, + "title": "Distance", + "side": "right" if vertical else "top" + }, + **axes_layouts}) fig.update_traces( showlegend=False, colorscale=colorscale, |