Update 07-forest_plot.ipynb

Many spelling and wording/layout changes. Still WIP

nbs/tutorials/07-forest_plot.ipynb

@@ -17,9 +17,9 @@
    "id": "cfdb7e31",
    "metadata": {},
    "source": [
-    "Version 2023.02.14, DABEST also supports the comparison and analysis of different delta-delta analysis through a function called \"forest_plot\". \n",
+    "Version 2023.02.14, DABEST now supports the comparison of different delta-delta or mini-meta analyses through a function called \"forest_plot\". \n",
     "\n",
-    "Many experimental designs investigate the effects of two interacting independent variables on a dependent variable. The delta-delta effect size enables us distill the net effect of the two variables. \n",
+    "Many experimental designs investigate the effects of two interacting independent variables on a dependent variable. The delta-delta effect size enables us to distill the net effect of the two variables. \n",
     "\n",
     "\n",
     "Consider 3 experiments where in each of the experiment we test the efficacy of 3 drugs named ``Drug1``, ``Drug2`` , and ``Drug3`` on a disease-causing mutation M based on disease metric Y. The greater the value Y has, the more severe the disease phenotype is. Phenotype Y has been shown to be caused by a gain-of-function mutation M, so we expect a difference between wild type (W) subjects and mutant subjects (M). Now, we want to know whether this effect is ameliorated by the administration of Drug treatment. We also administer a placebo as a control. In theory, we only expect Drug to have an effect on the M group, although in practice, many drugs have non-specific effects on healthy populations too."
@@ -349,40 +349,37 @@
    "id": "982afbdb",
    "metadata": {},
    "source": [
-    "Important Inputs:\n",
+    "Key Parameters:\n",
     "\n",
-    "1. A list of contrast objects \n",
+    "- ``contrasts``: A list of contrast objects \n",
     "\n",
-    "2. contrast_labels e.g. ``['Drug1', 'Drug2', 'Drug3']``\n",
+    "- ``contrast_type``: Select between ``\"delta2\"`` (for delta-delta) or ``\"mini_meta\"`` for mini-meta \n",
     "\n",
-    "3. title: default is ``\"ΔΔ Forest\"``\n",
+    "- ``contrast_labels``: A list of labels for the contrast objects. E.g., ``['Drug1', 'Drug2', 'Drug3']``\n",
     "\n",
-    "4. y_label: default as ``\"value\"``, please change it according to your measurement units/ types\n",
+    "- ``effect_size``: Select the effect size metric from ``\"mean_diff\", \"median_diff\", \"cliffs_delta\", \"cohens_d\", \
+     \"hedges_g\", or \"delta_g\"``. The default is ``\"mean_diff\"``\n",
     "\n",
-    "5. contrast_type ``delta-delta`` and ``mini-meta`` are supported\n",
+    "- ``ylabel``: The axis label of dependent variable (Y-axis for vertical layout, X-axis for horizontal layout). The default is ``\"value\"``\n",
     "\n",
-    "6. Which effect size to plot (default is ``delta-delta mean-diff``, but you can specify which effect size you want to use)\\n\n",
+    "- ``title``: The plot title. The default is ``\"ΔΔ Forest\"``\n",
     "\n",
-    "7. Axes to put the plot into existing figures \\n\n",
+    "- ``ax``: Specify a matplotlib axes to put the plot into existing figures \n",
     "\n",
-    "8. The argument ``horizontal`` is a boolean input (``True``/ ``False``) \\n\n",
+    "- ``horizontal``: A boolean input (``True``/ ``False``) to adjust the plot orientation. The default is vertical orientation (``False``) \n",
     "\n",
-    "   default is ``vertical``, (``False``) that changes the default orientation, \\n\n",
-    "   \n",
-    "   if ``True`` the delta-delta values will be reflected on the x axis and the delta plots will be plotted horizontally. \\n\n",
-    "9. Plot kwargs are supported such as violin plot kwargs, fontsize, marker_size, ci_line_width\n",
+    "- ``custom_palette`: A list of colors, one for each contrast object. E.g., ``[\'gray\', \'blue\', \'green\']``\n",
     "\n",
-    "output:\n",
+    "- Additional kwargs are supported such as ``violin_kwargs``, ``fontsize``, ``marker_size``, ``ci_line_width``, ``rotation_for_xlabels``, ``alpha_violin_plot``, ``remove_spines``, and ``additional_plotting_kwargs``\n",
     "\n",
-    "- A plot with horizontally/vertically laid out half violin plots of each of the prescribed delta bootstraps. \n"
    ]
   },
   {
    "cell_type": "markdown",
    "id": "06b93055",
    "metadata": {},
    "source": [
-    "#### Vertical (default) Layout"
+    "#### Vertical Layout (default)"
    ]
   },
   {
@@ -438,20 +435,6 @@
     "                                 horizontal=True);\n"
    ]
   },
-  {
-   "cell_type": "markdown",
-   "id": "dc49a603",
-   "metadata": {},
-   "source": [
-    "Additiionall, for aesthetics and labels, you can use:\n",
-    "\n",
-    "1. The ``custom_palette`` argument to specify the colors you would like to indicate each experiment in a list \\n\n",
-    "    e.g [\"gray\", \"blue\", \"green\" ].\n",
-    "    \n",
-    "2. Additionally. the argument ``ylabel`` should be specified to specify the unit or \n",
-    "    the exact name of the measurement of experiments, for example \"delta_deltas\", the default is \"value\""
-   ]
-  },
   {
    "cell_type": "markdown",
    "id": "4100ba2c",
@@ -480,7 +463,7 @@
    "source": [
     "forest2_vertical = forest_plot(paired_contrasts, \n",
     "                               contrast_labels =['Drug1', 'Drug2', 'Drug3'], \n",
-    "                               custom_palette= ['gray', 'blue', 'green' ], \n",
+    "                               custom_palette= ['gray', 'blue', 'green'], \n",
     "                               effect_size='delta_g');"
    ]
   },
@@ -505,7 +488,7 @@
     "\n",
     "forest2_horizontal = forest_plot(paired_contrasts, \n",
     "                                 contrast_labels =['Drug1', 'Drug2', 'Drug3'], \n",
-    "                                 custom_palette= ['gray', 'blue', 'green' ],\n",
+    "                                 custom_palette= ['gray', 'blue', 'green'],\n",
     "                                 horizontal=True, effect_size='delta_g');\n",
     "\n",
     "\n"
@@ -516,23 +499,15 @@
    "id": "6787aa97",
    "metadata": {},
    "source": [
-    "### Using existing axis \"ax\" as the optional input to plot forest_plot \\n\n",
-    "\n",
-    "\n",
-    "\n",
-    "With other kinds of dabest plots side by side or in other possible orientations, \\n\n",
-    "\n",
-    "We will specify the x_labels that we want to indicate in a list of strings and parse it as the argument contrast_labels, \\n\n",
-    "\n",
-    "for example ['Drug1', 'Drug2', 'Drug3']."
+    "## Embedding forest plots into existing axes with the ``ax`` parameter\n",
    ]
   },
   {
    "cell_type": "markdown",
    "id": "180cae3a",
    "metadata": {},
    "source": [
-    "### Two forest plots plotted together in one axis"
+    "### Two forest plots plotted together in one figure"
    ]
   },
   {
@@ -577,7 +552,7 @@
    "id": "829f0d03",
    "metadata": {},
    "source": [
-    "### Four different plots, 3 ``delta-delta`` and 1 ``forest plot``"
+    "### A forest plot added as a subfigure with a figure with a variety of DABEST plots"
    ]
   },
   {
@@ -652,9 +627,7 @@
    "id": "964471ab",
    "metadata": {},
    "source": [
-    "## Forest plot also supports:\n",
-    "\n",
-    "### ``mini-meta`` comparisons and with the contrast type changed to ``\"mini_meta_delta\"``"
+    "## Forest plot of mini-meta:\n",
    ]
   },
   {
@@ -742,15 +715,15 @@
    "id": "e04e1ac4",
    "metadata": {},
    "source": [
-    "## Use the contrast list and forest_plot() function to generate figures"
+    "## Generate the Figure"
    ]
   },
   {
    "cell_type": "markdown",
    "id": "c760a179",
    "metadata": {},
    "source": [
-    "### Verticle (default) Layout"
+    "### Vertical Layout (default)"
    ]
   },
   {