{ "cells": [ { "cell_type": "markdown", "metadata": { "tags": [] }, "source": [ "# Plotting univariate data\n", "\n", "(c) 2024–2025 Justin Bois. This work is licensed under a [Creative Commons Attribution License CC-BY 4.0](https://creativecommons.org/licenses/by/4.0/). All code contained herein is licensed under an [MIT license](https://opensource.org/licenses/MIT).\n", "\n", "This document was prepared at [Caltech](http://www.caltech.edu) with support financial support from the [Donna and Benjamin M. Rosen Bioengineering Center](http://rosen.caltech.edu).\n", "\n", "\n", "\n", "*This tutorial was generated from an Jupyter notebook. You can download the notebook [here](plotting_univariate_data.ipynb).*\n", "\n", "
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\n", " \n", " Loading BokehJS ...\n", "
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\n", "\n", "In this tutorial, we will explore plotting of data with one quantitative variable. Exactly what that means will become clear momentarily. For now, we will introduce a data set we will use for the plots.\n", "\n", "We will work with a data set from [Kleinteich and Gorb, Sci. Rep., 4, 5355, 2014](https://doi.org/10.1038/srep05225), and was featured in the [New York Times](http://www.nytimes.com/2014/08/25/science/a-frog-thats-a-living-breathing-pac-man.html). They measured several properties about the tongue strikes of horned frogs. Let’s take a look at the data set, which is in the file [frog_tongue_adhesion.csv](frog_tongue_adhesion.csv).\n", "\n", "We can load the data set in to a data frame and take a look." ] }, { "cell_type": "code", "execution_count": 2, "metadata": {}, "outputs": [ { "data": { "text/html": [ "
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dateIDtrial numberimpact force (mN)impact time (ms)impact force / body weightadhesive force (mN)time frog pulls on target (ms)adhesive force / body weightadhesive impulse (N-s)total contact area (mm2)contact area without mucus (mm2)contact area with mucus / contact area without mucuscontact pressure (Pa)adhesive strength (Pa)
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"2013_02_26""I"31205461.95-7858841.27-0.29387700.823117-2030
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" ], "text/plain": [ "shape: (5, 15)\n", "┌─────────────┬─────┬────────┬─────────────┬───┬────────────┬────────────┬────────────┬────────────┐\n", "│ date ┆ ID ┆ trial ┆ impact ┆ … ┆ contact ┆ contact ┆ contact ┆ adhesive │\n", "│ --- ┆ --- ┆ number ┆ force (mN) ┆ ┆ area ┆ area with ┆ pressure ┆ strength │\n", "│ str ┆ str ┆ --- ┆ --- ┆ ┆ without ┆ mucus / ┆ (Pa) ┆ (Pa) │\n", "│ ┆ ┆ i64 ┆ i64 ┆ ┆ mucus (mm… ┆ cont… ┆ --- ┆ --- │\n", "│ ┆ ┆ ┆ ┆ ┆ --- ┆ --- ┆ i64 ┆ i64 │\n", "│ ┆ ┆ ┆ ┆ ┆ i64 ┆ f64 ┆ ┆ │\n", "╞═════════════╪═════╪════════╪═════════════╪═══╪════════════╪════════════╪════════════╪════════════╡\n", "│ 2013_02_26 ┆ I ┆ 3 ┆ 1205 ┆ … ┆ 70 ┆ 0.82 ┆ 3117 ┆ -2030 │\n", "│ 2013_02_26 ┆ I ┆ 4 ┆ 2527 ┆ … ┆ 94 ┆ 0.07 ┆ 24923 ┆ -9695 │\n", "│ 2013_03_01 ┆ I ┆ 1 ┆ 1745 ┆ … ┆ 79 ┆ 0.05 ┆ 21020 ┆ -10239 │\n", "│ 2013_03_01 ┆ I ┆ 2 ┆ 1556 ┆ … ┆ 158 ┆ 0.52 ┆ 4718 ┆ -1381 │\n", "│ 2013_03_01 ┆ I ┆ 3 ┆ 493 ┆ … ┆ 216 ┆ 0.12 ┆ 2012 ┆ -3975 │\n", "└─────────────┴─────┴────────┴─────────────┴───┴────────────┴────────────┴────────────┴────────────┘" ] }, "execution_count": 2, "metadata": {}, "output_type": "execute_result" } ], "source": [ "df = pl.read_csv('frog_tongue_adhesion.csv', comment_prefix='#')\n", "\n", "# Have a look so we remember\n", "df.head()" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "## Plots with categorical variables\n", "\n", "Let us first consider the different kinds of data we may encounter as we think about constructing a plot.\n", "\n", "- **Quantitative** data may have continuously varying (and therefore ordered) values.\n", "- **Categorical** data has discrete, unordered values that a variable can take.\n", "- **Ordinal** data has discrete, ordered values. Integers are a classic example.\n", "- **Temporal** data refers to time, which can be represented as dates.\n", "\n", "In practice, ordinal data can be cast as quantitative or treated as categorical with an ordering enforced on the categories (e.g., categorical data `[1, 2, 3]` becomes `['1', '2', '3']`.). Temporal data can also be cast as quantitative, (e.g., second from the start time). We will therefore focus out attention on quantitative and categorical data.\n", "\n", "When we made scatter plots in the previous lesson, both types of data were quantitative. We did actually incorporate categorical information in the form of colors of the glyph (insomniacs and normal sleepers being colored differently) and in tooltips. \n", "\n", "But what if we wanted a single type of measurement, say impact force, for each frog? Here, we have the quantitative impact force data and the categorical frog ID data. One of our axes is now categorical." ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "## Bar graph\n", "\n", "To demonstrate how to set up a categorical axis with Bokeh, I will make a bar graph of the mean impact force for each of the four frogs. But before I even begin this, I will give you the following piece of advice: *Don't make bar graphs.* More on that in a moment.\n", "\n", "Before we do that, we need to compute the means from the inputted data frame." ] }, { "cell_type": "code", "execution_count": 3, "metadata": {}, "outputs": [ { "data": { "text/html": [ "
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IDimpact force (mN)
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"III"550.1
"IV"419.1
" ], "text/plain": [ "shape: (4, 2)\n", "┌─────┬───────────────────┐\n", "│ ID ┆ impact force (mN) │\n", "│ --- ┆ --- │\n", "│ str ┆ f64 │\n", "╞═════╪═══════════════════╡\n", "│ I ┆ 1530.2 │\n", "│ II ┆ 707.35 │\n", "│ III ┆ 550.1 │\n", "│ IV ┆ 419.1 │\n", "└─────┴───────────────────┘" ] }, "execution_count": 3, "metadata": {}, "output_type": "execute_result" } ], "source": [ "df_mean = (\n", " df\n", " .group_by('ID', maintain_order=True)\n", " .agg(pl.col('impact force (mN)').mean())\n", ")\n", "\n", "# Take a look\n", "df_mean" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "To set up a categorical axis, you need to specify the `x_range` (or `y_range` if you want the y-axis to be categorical) as a list with the categories you want on the axis when you instantiate the figure. I will make a horizontal bar graph, so I will specify `y_range`. Also, when I instantiate this figure, because it is not very tall and I do not want the reset tool cut off, I will also explicitly set the tools I want in the toolbar." ] }, { "cell_type": "code", "execution_count": 4, "metadata": {}, "outputs": [], "source": [ "p = bokeh.plotting.figure(\n", " frame_height=200,\n", " frame_width=400,\n", " x_axis_label='impact force (mN)',\n", " y_range=list(df_mean['ID'])[::-1],\n", " tools='pan,wheel_zoom,save,reset'\n", ")" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "Now that we have the figure, we can put the bars on. The `p.hbar()` method populates the figure with horizontal bar glyphs. The `right` kwarg says what column of the data source dictates how far to the right to show the bar, while the `height` kwarg says how think the bars are.\n", "\n", "I will also ensure the quantitative axis starts at zero and turn off the grid lines on the categorical axis, which is commonly done." ] }, { "cell_type": "code", "execution_count": 5, "metadata": {}, "outputs": [ { "data": { "text/html": [ "\n", "
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" console.log(\"Bokeh: ERROR: Unable to run BokehJS code because BokehJS library is missing\");\n", " }\n", " }\n", " }, 10, root)\n", " }\n", "})(window);" ], "application/vnd.bokehjs_exec.v0+json": "" }, "metadata": { "application/vnd.bokehjs_exec.v0+json": { "id": "p1001" } }, "output_type": "display_data" } ], "source": [ "p.hbar(\n", " source=df_mean.to_dict(),\n", " y='ID',\n", " right='impact force (mN)',\n", " height=0.6\n", ")\n", "\n", "# Turn off gridlines on categorical axis\n", "p.ygrid.grid_line_color = None\n", "\n", "# Start axes at origin on quantitative axis\n", "p.x_range.start = 0\n", "\n", "bokeh.io.show(p)" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "We similarly make vertical bar graphs specifying `x_range` and using `p.vbar()`." ] }, { "cell_type": "code", "execution_count": 6, "metadata": {}, "outputs": [ { "data": { "text/html": [ "\n", "
\n" ] }, "metadata": {}, "output_type": "display_data" }, { "data": { "application/javascript": [ "(function(root) {\n", " function embed_document(root) {\n", " const docs_json = {\"08fcd12e-d524-47f2-85c0-b90cbe30524e\":{\"version\":\"3.6.0\",\"title\":\"Bokeh 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force (mN)\",\"major_label_policy\":{\"type\":\"object\",\"name\":\"AllLabels\",\"id\":\"p1060\"}}}],\"below\":[{\"type\":\"object\",\"name\":\"CategoricalAxis\",\"id\":\"p1052\",\"attributes\":{\"ticker\":{\"type\":\"object\",\"name\":\"CategoricalTicker\",\"id\":\"p1053\"},\"formatter\":{\"type\":\"object\",\"name\":\"CategoricalTickFormatter\",\"id\":\"p1054\"},\"major_label_policy\":{\"type\":\"object\",\"name\":\"AllLabels\",\"id\":\"p1055\"}}}],\"center\":[{\"type\":\"object\",\"name\":\"Grid\",\"id\":\"p1056\",\"attributes\":{\"axis\":{\"id\":\"p1052\"},\"grid_line_color\":null}},{\"type\":\"object\",\"name\":\"Grid\",\"id\":\"p1061\",\"attributes\":{\"dimension\":1,\"axis\":{\"id\":\"p1057\"}}}],\"frame_width\":250,\"frame_height\":250}}]}};\n", " const render_items = [{\"docid\":\"08fcd12e-d524-47f2-85c0-b90cbe30524e\",\"roots\":{\"p1040\":\"faf8f4b7-a1cc-4711-b41f-01e6bcf5b5cc\"},\"root_ids\":[\"p1040\"]}];\n", " void root.Bokeh.embed.embed_items_notebook(docs_json, render_items);\n", " }\n", " if (root.Bokeh !== undefined) {\n", " embed_document(root);\n", " } else {\n", " let attempts = 0;\n", " const timer = setInterval(function(root) {\n", " if (root.Bokeh !== undefined) {\n", " clearInterval(timer);\n", " embed_document(root);\n", " } else {\n", " attempts++;\n", " if (attempts > 100) {\n", " clearInterval(timer);\n", " console.log(\"Bokeh: ERROR: Unable to run BokehJS code because BokehJS library is missing\");\n", " }\n", " }\n", " }, 10, root)\n", " }\n", "})(window);" ], "application/vnd.bokehjs_exec.v0+json": "" }, "metadata": { "application/vnd.bokehjs_exec.v0+json": { "id": "p1040" } }, "output_type": "display_data" } ], "source": [ "p = bokeh.plotting.figure(\n", " frame_height=250,\n", " frame_width=250,\n", " y_axis_label='impact force (mN)',\n", " x_range=list(df_mean['ID']),\n", ")\n", "\n", "p.vbar(\n", " source=df_mean.to_dict(),\n", " x='ID',\n", " top='impact force (mN)',\n", " width=0.6\n", ")\n", "\n", "p.xgrid.grid_line_color = None\n", "p.y_range.start = 0\n", "\n", "bokeh.io.show(p)" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "## iqplot\n", "\n", "Generating the bar graphs was not too painful, even tough we used Bokeh, a low-level plotting library. We would like to make plots more **declaratively**. We do not want to have to explicitly pre-process the data, set up the categorical axis, etc. We would like to just provide a data set, say which column(s) is/are categorical and which is quantitative, and then just get our plot. \n", "\n", "The [iqplot package](https://iqplot.github.io/) generates plots from tidy data frames where one or more columns contains categorical data and the column of interest in the plot is quantitative.\n", "\n", "There are seven (really four) types of plots that iqplot can generate. As you will see, all four of these modes of plotting are meant to give a picture about how the quantitative measurements are *distributed* for each category.\n", "\n", "+ Box plots: `iqplot.box()`\n", "+ Strip plots: `iqplot.strip()`\n", "+ Strip-box plots `iqplot.stripbox()`, which is an overlay of a strip and box plot\n", "+ Spike plots: `iqplot.spike()`\n", "+ Histograms: `iqplot.histogram()`\n", "+ Strip-histogram plots `iqplot.striphistogram()`, which is an overlay of a strip and box plot\n", "+ [ECDFs](https://en.wikipedia.org/wiki/Empirical_distribution_function): `iqplot.ecdf()`\n", " \n", "\n", "This first seven arguments are the same for all plots. They are:\n", "\n", "- `data`: A tidy data frame or Numpy array.\n", "- `q`: The column of the data frame to be treated as the quantitative variable.\n", "- `cats`: A list of columns in the data frame that are to be considered as categorical variables in the plot. If `None`, a single box, strip, histogram, or ECDF is plotted.\n", "- `q_axis`: Along which axis, x or y that the quantitative variable varies. The default is `'x'`.\n", "- `palette`: A list of hex colors to use for coloring the markers for each category. By default, it uses the Glasbey Category 10 color palette from [colorcet](https://colorcet.holoviz.org/).\n", "- `order`: If specified, the ordering of the categories to use on the categorical axis and legend (if applicable). Otherwise, the order of the inputted data frame is used.\n", "- `p`: If specified, the `bokeh.plotting.Figure` object to use for the plot. If not specified, a new figure is created.\n", "\n", "With this in mind, we will put iqplot to use on the frog data set." ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "## Box plots with iqplot\n", "\n", "As I [discuss below](#Don't-make-bar-graphs), bar graphs are almost never a good choice for visualization. You distill all of the information in the data set down to one or two summary statistics, and then use giant glyphs to show them. As a start for improvement, you could distill the data set down to five or so summary statistics and show those graphically, as opposed to just one or two. \n", "\n", "Box plots provide such a summary. I will first make one using `iqplot.box()` and then describe how a box plot is interpreted." ] }, { "cell_type": "code", "execution_count": 7, "metadata": {}, "outputs": [ { "data": { "text/html": [ "\n", "
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" console.log(\"Bokeh: ERROR: Unable to run BokehJS code because BokehJS library is missing\");\n", " }\n", " }\n", " }, 10, root)\n", " }\n", "})(window);" ], "application/vnd.bokehjs_exec.v0+json": "" }, "metadata": { "application/vnd.bokehjs_exec.v0+json": { "id": "p1089" } }, "output_type": "display_data" } ], "source": [ "p = iqplot.box(\n", " data=df,\n", " q=\"impact force (mN)\",\n", " cats=\"ID\",\n", ")\n", "\n", "bokeh.io.show(p)" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "The line in the middle of each box is the median and the top and bottom of the box at the 75th and 25th percentiles, respectively. The distance between the 25th and 75th percentiles is called the **interquartile range**, or IQR. The whiskers of the box plot extend to the most extreme data point within 1.5 times the interquartile range. If any data points are more extreme than the end of the whisker, they are shown individually, and are often referred to as _outliers_.\n", "\n", "A box plot can use a useful visualization if you have many data points and it is difficult to plot them all. I rarely find that there are situations where all data cannot be plotted, either with strip plots of ECDFs, which we will cover in a moment, so I generally do not use box plots. Nonetheless, I do not find them too objectionable, as they effectively display important nonparametric summary statistics of your data set." ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "## Plot all your data\n", "\n", "Box plots summarize a data set with summary statistics, but what not plot all your data? You work hard to acquire them. You should show them all. This is a mantra to live by.\n", "\n", "
\n", " \n", "Plot all of your data.\n", " \n", "
\n", "\n", "Let's do that now." ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "## Strip plots\n", "\n", "A **strip plot** is like a scatter plot; it puts a glyph for every measured data point. The only difference is that one of the axes is categorical. In this case, you are plotting all of your data." ] }, { "cell_type": "code", "execution_count": 8, "metadata": {}, "outputs": [ { "data": { "text/html": [ "\n", "
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" console.log(\"Bokeh: ERROR: Unable to run BokehJS code because BokehJS library is missing\");\n", " }\n", " }\n", " }, 10, root)\n", " }\n", "})(window);" ], "application/vnd.bokehjs_exec.v0+json": "" }, "metadata": { "application/vnd.bokehjs_exec.v0+json": { "id": "p1178" } }, "output_type": "display_data" } ], "source": [ "p = iqplot.strip(\n", " data=df,\n", " q=\"impact force (mN)\",\n", " cats=\"ID\",\n", " spread=None,\n", ")\n", "\n", "bokeh.io.show(p)" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "This is a good plot to make since you are plotting all of your data, but it does have the problem that you cannot tell if multiple data points overlap." ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "## Strip-box plots\n", "\n", "It is sometimes useful to overlay strip plots with box plots, as the box plots show useful quantile information. 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" console.log(\"Bokeh: ERROR: Unable to run BokehJS code because BokehJS library is missing\");\n", " }\n", " }\n", " }, 10, root)\n", " }\n", "})(window);" ], "application/vnd.bokehjs_exec.v0+json": "" }, "metadata": { "application/vnd.bokehjs_exec.v0+json": { "id": "p1227" } }, "output_type": "display_data" } ], "source": [ "p = iqplot.stripbox(\n", " data=df,\n", " q=\"impact force (mN)\",\n", " cats=\"ID\",\n", ")\n", "\n", "bokeh.io.show(p)" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "## Histograms\n", "\n", "In plotting all of our data in a strip plot, we can roughly see how the data are distributed. There are more measurements where there are more glyphs. We ofter seek to visualize the *distribution* of the data. **Histograms** are commonly used for this. They are typically interpreted to as an empirical representation of the probability density function." ] }, { "cell_type": "code", "execution_count": 10, "metadata": {}, "outputs": [ { "data": { "text/html": [ "\n", "
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ERROR: Unable to run BokehJS code because BokehJS library is missing\");\n", " }\n", " }\n", " }, 10, root)\n", " }\n", "})(window);" ], "application/vnd.bokehjs_exec.v0+json": "" }, "metadata": { "application/vnd.bokehjs_exec.v0+json": { "id": "p1340" } }, "output_type": "display_data" } ], "source": [ "p = iqplot.histogram(\n", " data=df,\n", " q=\"impact force (mN)\",\n", " cats=\"ID\",\n", ")\n", "\n", "bokeh.io.show(p)" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "Note that by default, iqplot includes a **rug plot** at the bottom of the histogram, showing each measurement." ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "## ECDFs\n", "\n", "I just mentioned that histograms are typically used to display how data are distributed, but it was hard to make out the distributions in the above plot, partly because we do not have very many measurements. As another example I will generate Normally distributed data and plot the histogram. (We will learn how to generate data like this when we study random number generation with NumPy in a future lesson. For now, this is for purposes of discussing plotting options.)\n", "\n", "Note that iqplot can take a Numpy array as the `data` argument, and makes a plot assuming it contains a single data set." ] }, { "cell_type": "code", "execution_count": 11, "metadata": {}, "outputs": [ { "data": { "text/html": [ "\n", "
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"x = rng.normal(size=500)\n", "\n", "# Plot the histogram\n", "p = iqplot.histogram(x, rug=False)\n", "\n", "bokeh.io.show(p)" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "This looks similar to the standard Normal curve we are used to seeing and is a useful comparison to a **probability density function** (PDF). However, Histograms suffer from **binning bias**. By binning the data, you are not plotting all of them. In general, if you can **plot all of your data**, you should. For that reason, I prefer not to use histograms for studying how data are distributed, but rather prefer to use ECDFs, which enable plotting of all data.\n", "\n", "The ECDF evaluated at x for a set of measurements is defined as\n", "\n", "\\begin{align}\n", "\\text{ECDF}(x) = \\text{fraction of measurements } \\le x.\n", "\\end{align}\n", "\n", "While the histogram is an attempt to visualize a probability density function (PDF) of a distribution, the ECDF visualizes the **cumulative density function** (CDF). The CDF, $F(x)$, and PDF, $f(x)$, both completely define a univariate distribution and are related by\n", "\n", "\\begin{align}\n", "f(x) = \\frac{\\mathrm{d}F}{\\mathrm{d}x}.\n", "\\end{align}\n", "\n", "The definition of the ECDF is all that you need for interpretation. Once you get used to looking at CDFs, they will become as familiar to you as PDFs. A peak in a PDF corresponds to an inflection point in a CDF.\n", "\n", "To make this more clear, let us look at plot of a PDF and ECDF for familiar distributions, the Gaussian and Binomial.\n", "\n", "
\n", "\n", "![PDF/CDF](pdf_cdf.png)\n", " \n", "
\n", "\n", "Now that we know how to interpret ECDFs, lets plot the ECDF for our dummy Normally-distributed data." ] }, { "cell_type": "code", "execution_count": 12, "metadata": {}, "outputs": [ { "data": { "text/html": [ "\n", "
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"metadata": {}, "source": [ "Now that we understand what an ECDF is and how to plot it, let's make a set of ECDFs for our frog data." ] }, { "cell_type": "code", "execution_count": 13, "metadata": {}, "outputs": [ { "data": { "text/html": [ "\n", "
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ERROR: Unable to run BokehJS code because BokehJS library is missing\");\n", " }\n", " }\n", " }, 10, root)\n", " }\n", "})(window);" ], "application/vnd.bokehjs_exec.v0+json": "" }, "metadata": { "application/vnd.bokehjs_exec.v0+json": { "id": "p1979" } }, "output_type": "display_data" } ], "source": [ "p = iqplot.ecdf(\n", " data=df,\n", " q=\"impact force (mN)\",\n", " cats=\"ID\",\n", " style='dots',\n", " p=p,\n", " show_legend=False,\n", ")\n", "\n", "bokeh.io.show(p)" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "## Customization with iqplot\n", "\n", "You may have noticed in the discussion of ECDFs that I introduced some new keyword arguments, `style` and `p`. In fact, each of the plotting functions also has the following additional optional keyword arguments, as described above.\n", "\n", "- `q_axis`: Along which axis, x or y that the quantitative variable varies. The default is `'x'`.\n", "- `palette`: A list of hex colors to use for coloring the markers for each category. By default, it uses the Glasbey Category 10 color palette from [colorcet](https://colorcet.holoviz.org/).\n", "- `order`: If specified, the ordering of the categories to use on the categorical axis and legend (if applicable). Otherwise, the order of the inputted data frame is used.\n", "- `p`: If specified, the `bokeh.plotting.Figure` object to use for the plot. If not specified, a new figure is created.\n", "\n", "The respective plotting functions also have kwargs that are specific to each (such as `style` for `iqplot.ecdf()`. Examples highlighting some, but not all, customizations follow. You can find out what kwargs are available for each function by reading their doc strings, e.g., with\n", "\n", "```python\n", "iqplot.box?\n", "```\n", "\n", "Any kwargs not in the function call signature are passed to `bokeh.plotting.figure()` when the figure is instantiated." ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "### Customizing box plots\n", "\n", "We can also have vertical box plots." ] }, { "cell_type": "code", "execution_count": 15, "metadata": {}, "outputs": [ { "data": { "text/html": [ "\n", "
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render_items);\n", " }\n", " if (root.Bokeh !== undefined) {\n", " embed_document(root);\n", " } else {\n", " let attempts = 0;\n", " const timer = setInterval(function(root) {\n", " if (root.Bokeh !== undefined) {\n", " clearInterval(timer);\n", " embed_document(root);\n", " } else {\n", " attempts++;\n", " if (attempts > 100) {\n", " clearInterval(timer);\n", " console.log(\"Bokeh: ERROR: Unable to run BokehJS code because BokehJS library is missing\");\n", " }\n", " }\n", " }, 10, root)\n", " }\n", "})(window);" ], "application/vnd.bokehjs_exec.v0+json": "" }, "metadata": { "application/vnd.bokehjs_exec.v0+json": { "id": "p2251" } }, "output_type": "display_data" } ], "source": [ "p = iqplot.box(\n", " data=df,\n", " q=\"impact force (mN)\",\n", " cats=\"ID\",\n", " q_axis='y',\n", ")\n", "\n", "bokeh.io.show(p)" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "We can independently specify properties of the marks using `box_kwargs`, `whisker_kwargs`, `median_kwargs`, and `outlier_kwargs`. For example, say we wanted our colors to be [Betancourt red](https://betanalpha.github.io/assets/case_studies/principled_bayesian_workflow.html#step_four:_build_a_generative_model19), and that we wanted the outliers to also be that color and use diamond glyphs." ] }, { "cell_type": "code", "execution_count": 16, "metadata": {}, "outputs": [ { "data": { "text/html": [ "\n", "
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force (mN)\",\"major_label_policy\":{\"type\":\"object\",\"name\":\"AllLabels\",\"id\":\"p2354\"}}}],\"center\":[{\"type\":\"object\",\"name\":\"Grid\",\"id\":\"p2355\",\"attributes\":{\"axis\":{\"id\":\"p2351\"}}},{\"type\":\"object\",\"name\":\"Grid\",\"id\":\"p2360\",\"attributes\":{\"dimension\":1,\"axis\":{\"id\":\"p2356\"},\"grid_line_color\":null}}],\"frame_width\":375,\"frame_height\":275}}]}};\n", " const render_items = [{\"docid\":\"f3b5bbc2-0a8d-487f-a57a-5332dd0adb90\",\"roots\":{\"p2340\":\"a74e27a2-3abb-47f8-befd-1ae5956dab98\"},\"root_ids\":[\"p2340\"]}];\n", " void root.Bokeh.embed.embed_items_notebook(docs_json, render_items);\n", " }\n", " if (root.Bokeh !== undefined) {\n", " embed_document(root);\n", " } else {\n", " let attempts = 0;\n", " const timer = setInterval(function(root) {\n", " if (root.Bokeh !== undefined) {\n", " clearInterval(timer);\n", " embed_document(root);\n", " } else {\n", " attempts++;\n", " if (attempts > 100) {\n", " clearInterval(timer);\n", " console.log(\"Bokeh: ERROR: Unable to run BokehJS code because BokehJS library is missing\");\n", " }\n", " }\n", " }, 10, root)\n", " }\n", "})(window);" ], "application/vnd.bokehjs_exec.v0+json": "" }, "metadata": { "application/vnd.bokehjs_exec.v0+json": { "id": "p2340" } }, "output_type": "display_data" } ], "source": [ "p = iqplot.box(\n", " data=df,\n", " q=\"impact force (mN)\",\n", " cats=\"ID\",\n", " whisker_caps=True,\n", " outlier_marker='diamond',\n", " box_kwargs=dict(fill_color='#7C0000'),\n", " whisker_kwargs=dict(line_color='#7C0000', line_width=2),\n", ")\n", "\n", "bokeh.io.show(p)" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "### Customizing strip plots\n", "\n", "To help alleviate the overlap problem, we can make a strip plot with dash markers and add some transparency." ] }, { "cell_type": "code", "execution_count": 17, "metadata": {}, "outputs": [ { "data": { "text/html": [ "\n", "
\n" ] }, "metadata": {}, "output_type": "display_data" }, { "data": { "application/javascript": [ "(function(root) {\n", " function embed_document(root) {\n", " const docs_json = {\"d21ae698-078b-4658-8734-25b57da75d4a\":{\"version\":\"3.6.0\",\"title\":\"Bokeh 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" console.log(\"Bokeh: ERROR: Unable to run BokehJS code because BokehJS library is missing\");\n", " }\n", " }\n", " }, 10, root)\n", " }\n", "})(window);" ], "application/vnd.bokehjs_exec.v0+json": "" }, "metadata": { "application/vnd.bokehjs_exec.v0+json": { "id": "p2444" } }, "output_type": "display_data" } ], "source": [ "p = iqplot.strip(\n", " data=df,\n", " q=\"impact force (mN)\",\n", " cats=\"ID\",\n", " marker='dash',\n", " marker_kwargs=dict(alpha=0.5)\n", ")\n", "\n", "bokeh.io.show(p)" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "The problem with strip plots is that they can have trouble with overlapping data points. 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console.log(\"Bokeh: ERROR: Unable to run BokehJS code because BokehJS library is missing\");\n", " }\n", " }\n", " }, 10, root)\n", " }\n", "})(window);" ], "application/vnd.bokehjs_exec.v0+json": "" }, "metadata": { "application/vnd.bokehjs_exec.v0+json": { "id": "p2493" } }, "output_type": "display_data" } ], "source": [ "p = iqplot.strip(\n", " data=df,\n", " q=\"impact force (mN)\",\n", " cats=\"ID\",\n", " spread=\"jitter\",\n", " tooltips=[\n", " ('trial', '@{trial number}'),\n", " ('adh force', '@{adhesive force (mN)}')\n", " ],\n", ")\n", "\n", "bokeh.io.show(p)" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "With any of the plots, you can have more than one categorical column, and the categorical axes are nicely spaced and formatted. Here, we'll categorize by frog ID and by trial number." ] }, { "cell_type": "code", "execution_count": 19, "metadata": {}, "outputs": [ { "data": { "text/html": [ "\n", "
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number\",\"click_policy\":\"hide\",\"items\":[{\"type\":\"object\",\"name\":\"LegendItem\",\"id\":\"p2639\",\"attributes\":{\"label\":{\"type\":\"value\",\"value\":\"1\"},\"renderers\":[{\"id\":\"p2587\"}]}},{\"type\":\"object\",\"name\":\"LegendItem\",\"id\":\"p2640\",\"attributes\":{\"label\":{\"type\":\"value\",\"value\":\"2\"},\"renderers\":[{\"id\":\"p2599\"}]}},{\"type\":\"object\",\"name\":\"LegendItem\",\"id\":\"p2641\",\"attributes\":{\"label\":{\"type\":\"value\",\"value\":\"3\"},\"renderers\":[{\"id\":\"p2611\"}]}},{\"type\":\"object\",\"name\":\"LegendItem\",\"id\":\"p2642\",\"attributes\":{\"label\":{\"type\":\"value\",\"value\":\"4\"},\"renderers\":[{\"id\":\"p2623\"}]}},{\"type\":\"object\",\"name\":\"LegendItem\",\"id\":\"p2643\",\"attributes\":{\"label\":{\"type\":\"value\",\"value\":\"5\"},\"renderers\":[{\"id\":\"p2635\"}]}}]}}],\"below\":[{\"type\":\"object\",\"name\":\"LinearAxis\",\"id\":\"p2555\",\"attributes\":{\"ticker\":{\"type\":\"object\",\"name\":\"BasicTicker\",\"id\":\"p2556\",\"attributes\":{\"mantissas\":[1,2,5]}},\"formatter\":{\"type\":\"object\",\"name\":\"BasicTickFormatter\",\"id\":\"p2557\"},\"axis_label\":\"impact force (mN)\",\"major_label_policy\":{\"type\":\"object\",\"name\":\"AllLabels\",\"id\":\"p2558\"}}}],\"center\":[{\"type\":\"object\",\"name\":\"Grid\",\"id\":\"p2559\",\"attributes\":{\"axis\":{\"id\":\"p2555\"}}},{\"type\":\"object\",\"name\":\"Grid\",\"id\":\"p2564\",\"attributes\":{\"dimension\":1,\"axis\":{\"id\":\"p2560\"},\"grid_line_color\":null}}],\"frame_height\":275}}]}};\n", " const render_items = [{\"docid\":\"c8a601ff-47db-42bd-93eb-a34e7ad2f534\",\"roots\":{\"p2544\":\"f826cfbd-e937-4753-b853-9668d765ad32\"},\"root_ids\":[\"p2544\"]}];\n", " void root.Bokeh.embed.embed_items_notebook(docs_json, render_items);\n", " }\n", " if (root.Bokeh !== undefined) {\n", " embed_document(root);\n", " } else {\n", " let attempts = 0;\n", " const timer = setInterval(function(root) {\n", " if (root.Bokeh !== undefined) {\n", " clearInterval(timer);\n", " embed_document(root);\n", " } else {\n", " attempts++;\n", " if (attempts > 100) {\n", " clearInterval(timer);\n", " console.log(\"Bokeh: ERROR: Unable to run BokehJS code because BokehJS library is missing\");\n", " }\n", " }\n", " }, 10, root)\n", " }\n", "})(window);" ], "application/vnd.bokehjs_exec.v0+json": "" }, "metadata": { "application/vnd.bokehjs_exec.v0+json": { "id": "p2544" } }, "output_type": "display_data" } ], "source": [ "p = iqplot.strip(\n", " data=df,\n", " q=\"impact force (mN)\",\n", " cats=['ID', 'trial number'],\n", " color_column='trial number',\n", " width=550,\n", ")\n", "\n", "bokeh.io.show(p)" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "### Customizing histograms\n", "\n", "We could plot normalized histograms using the density kwarg." ] }, { "cell_type": "code", "execution_count": 20, "metadata": {}, "outputs": [ { "data": { "text/html": [ "\n", "
\n" ] }, "metadata": {}, "output_type": "display_data" }, { "data": { "application/javascript": [ "(function(root) {\n", " function embed_document(root) {\n", " const docs_json = {\"128aa4e5-8297-4e78-a7ce-c82b8c73ab44\":{\"version\":\"3.6.0\",\"title\":\"Bokeh 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" const render_items = [{\"docid\":\"128aa4e5-8297-4e78-a7ce-c82b8c73ab44\",\"roots\":{\"p2655\":\"ca66836f-4c7d-4d11-8ff5-15b2d195bfb3\"},\"root_ids\":[\"p2655\"]}];\n", " void root.Bokeh.embed.embed_items_notebook(docs_json, render_items);\n", " }\n", " if (root.Bokeh !== undefined) {\n", " embed_document(root);\n", " } else {\n", " let attempts = 0;\n", " const timer = setInterval(function(root) {\n", " if (root.Bokeh !== undefined) {\n", " clearInterval(timer);\n", " embed_document(root);\n", " } else {\n", " attempts++;\n", " if (attempts > 100) {\n", " clearInterval(timer);\n", " console.log(\"Bokeh: ERROR: Unable to run BokehJS code because BokehJS library is missing\");\n", " }\n", " }\n", " }, 10, root)\n", " }\n", "})(window);" ], "application/vnd.bokehjs_exec.v0+json": "" }, "metadata": { "application/vnd.bokehjs_exec.v0+json": { "id": "p2655" } }, "output_type": "display_data" } ], "source": [ "# Plot the histogram\n", "p = iqplot.histogram(x, density=True, rug=False)\n", "\n", "bokeh.io.show(p)" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "### Customizing ECDFs\n", "\n", "Instead of plotting a separate ECDF for each category, we can put all of the categories together on one ECDF and color the points by the categorical variable by using the `kind='colored'` kwarg. Note that if we do this, we can only have the \"dot\" style ECDF, not the staircase." ] }, { "cell_type": "code", "execution_count": 21, "metadata": {}, "outputs": [ { "data": { "text/html": [ "\n", "
\n" ] }, "metadata": {}, "output_type": "display_data" }, { "data": { "application/javascript": [ "(function(root) {\n", " function embed_document(root) {\n", " const docs_json = {\"451c9b66-9e66-4731-afa3-5e1bad8552c4\":{\"version\":\"3.6.0\",\"title\":\"Bokeh 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ERROR: Unable to run BokehJS code because BokehJS library is missing\");\n", " }\n", " }\n", " }, 10, root)\n", " }\n", "})(window);" ], "application/vnd.bokehjs_exec.v0+json": "" }, "metadata": { "application/vnd.bokehjs_exec.v0+json": { "id": "p2700" } }, "output_type": "display_data" } ], "source": [ "p = iqplot.ecdf(\n", " data=df,\n", " q=\"impact force (mN)\",\n", " cats=\"ID\",\n", " kind='colored',\n", " tooltips=[\n", " ('trial', '@{trial number}'),\n", " ('adh force', '@{adhesive force (mN)}')\n", " ], \n", ")\n", "\n", "bokeh.io.show(p)" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "## Don't make bar graphs\n", "\n", "Bar graphs, especially with error bars (in which case they are called dynamite plots), are typically awful. They are pervasive in biology papers. I have yet to find a single example where a bar graph is the best choice. Strip plots (with jitter) or even box plots, are more informative and almost always preferred. In fact, ECDFs are often better even than these. Here is a simple message:\n", "\n", "
\n", " \n", "Don't make bar graphs.\n", " \n", "
\n", "\n", "What should I do instead you ask? The answer is simple: **plot all of your data** when you can. If you can't, box plots are always better than bar graphs." ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "## Computing environment" ] }, { "cell_type": "code", "execution_count": 22, "metadata": { "tags": [ "hide-input" ] }, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "Python implementation: CPython\n", "Python version : 3.12.5\n", "IPython version : 8.27.0\n", "\n", "numpy : 1.26.4\n", "polars : 1.8.2\n", "bokeh : 3.6.0\n", "iqplot : 0.3.7\n", "jupyterlab: 4.2.5\n", "\n" ] } ], "source": [ "%load_ext watermark\n", "%watermark -v -p numpy,polars,bokeh,iqplot,jupyterlab" ] } ], "metadata": { "kernelspec": { "display_name": "Python 3 (ipykernel)", "language": "python", "name": "python3" }, "language_info": { "codemirror_mode": { "name": "ipython", "version": 3 }, "file_extension": ".py", "mimetype": "text/x-python", "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", "version": "3.12.5" } }, "nbformat": 4, "nbformat_minor": 4 }