diff options
| -rw-r--r-- | gn3/heatmaps.py (renamed from gn3/computations/heatmap.py) | 25 | ||||
| -rw-r--r-- | gn3/heatmaps/heatmaps.py | 67 | ||||
| -rw-r--r-- | tests/unit/test_heatmaps.py (renamed from tests/unit/computations/test_heatmap.py) | 4 |
3 files changed, 27 insertions, 69 deletions
diff --git a/gn3/computations/heatmap.py b/gn3/heatmaps.py index 8727c92..198fb45 100644 --- a/gn3/computations/heatmap.py +++ b/gn3/heatmaps.py @@ -275,3 +275,28 @@ def get_nearest_marker(traits_list, genotype): marker_finder = nearest_marker_finder(genotype) return [marker_finder(trait) for trait in traits_list] + +# # Grey + Blue + Red +# def generate_heatmap(): +# cols = 20 +# y_axis = (["%s"%x for x in range(1, cols+1)][:-1] + ["X"]) #replace last item with x for now +# x_axis = heatmap_x_axis_names() +# data = generate_random_data(height=cols, width=len(x_axis)) +# fig = px.imshow( +# data, +# x=x_axis, +# y=y_axis, +# width=500) +# fig.update_traces(xtype="array") +# fig.update_traces(ytype="array") +# # fig.update_traces(xgap=10) +# fig.update_xaxes( +# visible=True, +# title_text="Traits", +# title_font_size=16) +# fig.update_layout( +# coloraxis_colorscale=[ +# [0.0, '#3B3B3B'], [0.4999999999999999, '#ABABAB'], +# [0.5, '#F5DE11'], [1.0, '#FF0D00']]) +# fig.write_html("%s/%s"%(heatmap_dir, "test_image.html")) +# return fig diff --git a/gn3/heatmaps/heatmaps.py b/gn3/heatmaps/heatmaps.py deleted file mode 100644 index 88f546d..0000000 --- a/gn3/heatmaps/heatmaps.py +++ /dev/null @@ -1,67 +0,0 @@ -import random -import plotly.express as px - -#### Remove these #### - -heatmap_dir = "heatmap_images" - -def generate_random_data(data_stop: float = 2, width: int = 10, height: int = 30): - """ - This is mostly a utility function to be used to generate random data, useful - for development of the heatmap generation code, without access to the actual - database data. - """ - return [[random.uniform(0,data_stop) for i in range(0, width)] - for j in range(0, height)] - -def generate_random_data2(data_stop: float = 2, width: int = 10, height: int = 30): - """ - This is mostly a utility function to be used to generate random data, useful - for development of the heatmap generation code, without access to the actual - database data. - """ - return [ - [{ - "value": item, - "category": random.choice(["C57BL/6J +", "DBA/2J +"])} - for item in axis] - for axis in generate_random_data(data_stop, width, height)] - -def heatmap_x_axis_names(): - return [ - "UCLA_BXDBXH_CARTILAGE_V2::ILM103710672", - "UCLA_BXDBXH_CARTILAGE_V2::ILM2260338", - "UCLA_BXDBXH_CARTILAGE_V2::ILM3140576", - "UCLA_BXDBXH_CARTILAGE_V2::ILM5670577", - "UCLA_BXDBXH_CARTILAGE_V2::ILM2070121", - "UCLA_BXDBXH_CARTILAGE_V2::ILM103990541", - "UCLA_BXDBXH_CARTILAGE_V2::ILM1190722", - "UCLA_BXDBXH_CARTILAGE_V2::ILM6590722", - "UCLA_BXDBXH_CARTILAGE_V2::ILM4200064", - "UCLA_BXDBXH_CARTILAGE_V2::ILM3140463"] -#### END: Remove these #### - -# Grey + Blue + Red -def generate_heatmap(): - cols = 20 - y_axis = (["%s"%x for x in range(1, cols+1)][:-1] + ["X"]) #replace last item with x for now - x_axis = heatmap_x_axis_names() - data = generate_random_data(height=cols, width=len(x_axis)) - fig = px.imshow( - data, - x=x_axis, - y=y_axis, - width=500) - fig.update_traces(xtype="array") - fig.update_traces(ytype="array") - # fig.update_traces(xgap=10) - fig.update_xaxes( - visible=True, - title_text="Traits", - title_font_size=16) - fig.update_layout( - coloraxis_colorscale=[ - [0.0, '#3B3B3B'], [0.4999999999999999, '#ABABAB'], - [0.5, '#F5DE11'], [1.0, '#FF0D00']]) - fig.write_html("%s/%s"%(heatmap_dir, "test_image.html")) - return fig diff --git a/tests/unit/computations/test_heatmap.py b/tests/unit/test_heatmaps.py index 156af45..265d5a8 100644 --- a/tests/unit/computations/test_heatmap.py +++ b/tests/unit/test_heatmaps.py @@ -1,6 +1,6 @@ -"""Module contains tests for gn3.computations.heatmap""" +"""Module contains tests for gn3.heatmaps.heatmaps""" from unittest import TestCase -from gn3.computations.heatmap import ( +from gn3.heatmaps import ( cluster_traits, export_trait_data, compute_traits_order, |