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JAnns98JAnns98
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forest_plot can now be accessed directly from dabest
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+37
-37
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2 files changed

+37
-37
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‎dabest/__init__.py

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@@ -3,6 +3,7 @@
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from ._stats_tools import confint_2group_diff as ci_2g
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from ._effsize_objects import TwoGroupsEffectSize, PermutationTest
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from ._dabest_object import Dabest
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from .forest_plot import forest_plot
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import os

‎nbs/tutorials/07-forest_plot.ipynb

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@@ -43,7 +43,7 @@
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"name": "stderr",
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"output_type": "stream",
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"text": [
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"Compiling numba functions: 100%|██████████| 11/11 [00:03<00:00, 2.83it/s]\n"
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"Compiling numba functions: 100%|██████████| 11/11 [00:00<00:00, 50.19it/s]"
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]
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},
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{
@@ -53,13 +53,19 @@
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"Numba compilation complete!\n",
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"We're using DABEST v2025.03.14\n"
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]
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},
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{
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"name": "stderr",
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"output_type": "stream",
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"text": [
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"\n"
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]
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}
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],
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"source": [
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"import numpy as np\n",
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"import pandas as pd\n",
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"import dabest\n",
62-
"from dabest.forest_plot import forest_plot\n",
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"import matplotlib.pyplot as plt\n",
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"import dabest \n",
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"print(\"We're using DABEST v{}\".format(dabest.__version__))"
@@ -328,7 +334,7 @@
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}
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],
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"source": [
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"f_forest_delta2 = forest_plot(\n",
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"f_forest_delta2 = dabest.forest_plot(\n",
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" data = contrasts, \n",
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" labels = ['Drug1', 'Drug2', 'Drug3']\n",
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");"
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}
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],
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"source": [
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"f_forest_delta2 = forest_plot(\n",
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"f_forest_delta2 = dabest.forest_plot(\n",
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" data = contrasts, \n",
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" labels = ['Drug1 Delta1', 'Drug1 Delta-Delta', 'Drug2 Delta1', 'Drug2 Delta-Delta', 'Drug3 Delta1', 'Drug3 Delta-Delta'],\n",
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" idx=[[0, 2], [0, 2], [0, 2]]\n",
@@ -417,20 +423,20 @@
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}
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],
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"source": [
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"f_forest_delta2 = forest_plot(\n",
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" data = contrasts, \n",
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" labels = ['Drug1', 'Drug2', 'Drug3'],\n",
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" effect_size='hedges_g');\n",
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"f_forest_delta2 = forest_plot(\n",
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" data = contrasts, \n",
426-
" labels = ['Drug1', 'Drug2', 'Drug3'],\n",
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" effect_size='delta_g');\n",
426+
"f_forest_delta2 = dabest.forest_plot(\n",
427+
" data = contrasts, \n",
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" labels = ['Drug1', 'Drug2', 'Drug3'],\n",
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" effect_size='hedges_g');\n",
430+
"f_forest_delta2 = dabest.forest_plot(\n",
431+
" data = contrasts, \n",
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" labels = ['Drug1', 'Drug2', 'Drug3'],\n",
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" effect_size='delta_g');\n",
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"\n",
429-
"f_forest_delta2 = forest_plot(\n",
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" data = contrasts, \n",
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" labels = ['Drug1 Delta1', 'Drug1 Delta-Delta', 'Drug2 Delta1', 'Drug2 Delta-Delta', 'Drug3 Delta1', 'Drug3 Delta-Delta'],\n",
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" effect_size='hedges_g',\n",
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" idx=[[0, 2], [0, 2], [0, 2]]);"
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"f_forest_delta2 = dabest.forest_plot(\n",
436+
" data = contrasts, \n",
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" labels = ['Drug1 Delta1', 'Drug1 Delta-Delta', 'Drug2 Delta1', 'Drug2 Delta-Delta', 'Drug3 Delta1', 'Drug3 Delta-Delta'],\n",
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" effect_size='hedges_g',\n",
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" idx=[[0, 2], [0, 2], [0, 2]]);"
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]
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},
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{
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}
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],
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"source": [
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"f_forest_minimeta = forest_plot(\n",
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" data = contrasts_mini_meta, \n",
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" labels=['mini_meta1', 'mini_meta2', 'mini_meta3']\n",
560+
"f_forest_minimeta = dabest.forest_plot(\n",
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" data = contrasts_mini_meta, \n",
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" labels=['mini_meta1', 'mini_meta2', 'mini_meta3']\n",
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");"
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]
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},
@@ -587,20 +593,13 @@
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}
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],
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"source": [
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"f_forest_minimeta = forest_plot(\n",
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"f_forest_minimeta = dabest.forest_plot(\n",
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" data = contrasts_mini_meta, \n",
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" idx = [[0, 3],[0, 3], [0, 3]],\n",
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" labels=['Contrast 1A', 'mini_meta1', 'Contrast 2A', 'mini_meta2', 'Contrast 3A', 'mini_meta3']\n",
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");"
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]
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},
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{
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"cell_type": "code",
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"execution_count": null,
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"metadata": {},
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"outputs": [],
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"source": []
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},
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{
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"cell_type": "markdown",
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"metadata": {},
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}
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],
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"source": [
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"forest_plot(contrasts_deltas, idx=((0,),(0,), (0,)), \n",
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"dabest.forest_plot(contrasts_deltas, idx=((0,),(0,), (0,)), \n",
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" labels=['Drug1 \\nTest 1 - Control 1', 'Drug2 \\nTest 2 - Control 2', 'Drug3 \\nTest 3 - Control 3']);"
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]
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},
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}
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],
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"source": [
735-
"f_forest_minimeta = forest_plot(\n",
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"f_forest_minimeta = dabest.forest_plot(\n",
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" data = contrasts_mini_meta, \n",
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" labels=['mini_meta1', 'mini_meta2', 'mini_meta3'],\n",
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" horizontal=True,)"
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}
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],
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"source": [
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"f_forest_minimeta = forest_plot(\n",
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"f_forest_minimeta = dabest.forest_plot(\n",
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" data = contrasts_mini_meta, \n",
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" labels=['mini_meta1', 'mini_meta2', 'mini_meta3'],\n",
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" custom_palette=['#FF0000', '#00FF00', '#0000FF'],)"
@@ -794,7 +793,7 @@
794793
}
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],
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"source": [
797-
"f_forest_hedgesg = forest_plot(\n",
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"f_forest_hedgesg = dabest.forest_plot(\n",
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" data = contrasts, \n",
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" labels =['Drug1', 'Drug2', 'Drug3'], \n",
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" effect_size='hedges_g',\n",
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}
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],
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"source": [
829-
"f_forest_minimeta = forest_plot(\n",
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"f_forest_minimeta = dabest.forest_plot(\n",
830829
" data = contrasts_mini_meta, \n",
831830
" labels=['mini_meta1', 'mini_meta2', 'mini_meta3'],\n",
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" custom_palette=['#FF0000', '#00FF00', '#0000FF'],\n",
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}
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],
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"source": [
872-
"f_forest_minimeta = forest_plot(\n",
871+
"f_forest_minimeta = dabest.forest_plot(\n",
873872
" data = contrasts_mini_meta, \n",
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" labels=['mini_meta1', 'mini_meta2', 'mini_meta3'],\n",
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" custom_palette=['#FF0000', '#00FF00', '#0000FF'],\n",
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906905
}
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],
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"source": [
909-
"f_forest_minimeta = forest_plot(\n",
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"f_forest_minimeta = dabest.forest_plot(\n",
910909
" data = contrasts_mini_meta, \n",
911910
" labels=['mini_meta1', 'mini_meta2', 'mini_meta3'],\n",
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" custom_palette=['#FF0000', '#00FF00', '#0000FF'],\n",
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}
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],
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"source": [
942-
"f_forest_minimeta = forest_plot(\n",
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"f_forest_minimeta = dabest.forest_plot(\n",
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" data = contrasts_mini_meta, \n",
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" labels=['mini_meta1', 'mini_meta2', 'mini_meta3'],\n",
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" custom_palette=['#FF0000', '#00FF00', '#0000FF'],\n",
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" ax = ax\n",
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" )\n",
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"\n",
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"forest_plot(\n",
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"dabest.forest_plot(\n",
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" data = contrasts, \n",
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" labels = ['Drug1', 'Drug2', 'Drug3'], \n",
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" ax = axes[1,1], \n",

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