Update README and add plots to examples. Also clean up the cord19 exa…

…mple.

README.rst

@@ -9,7 +9,84 @@
 DataMapPlot
 ===========
 
-Creating beautiful plots of data maps. This provides basic tools for generating presentation or publication worthy 
-static plots of labelled data maps. All you need to do is label clusters of points in the data map and DataMapPlot
-will take care of the rest. There are a number of options for tweaking the results, but the aim is to have something 
-good-looking straight out-of-the-box.
+Creating beautiful plots of data maps. DataMapPlot is a small library designed to help you make beautiful data map
+plots for inclusion in presentations, posters and papers. The focus is on producing static plots that are great
+looking with as little work for you as possible. All you need to do is label clusters of points in the data map and
+DataMapPlot will take care of the rest. While this involves automating most of the aesthetic choices, the library
+provides a wide variety of ways to customize the resulting plot to your needs.
+
+--------
+Examples
+--------
+
+Some examples of the kind of output that DataMapPlot can provide.
+
+A basic plot, with soem highlighted labels:
+
+.. image:: examples/plot_cord19.png
+   :width: 1024
+   :alt: A data map plot of the CORD-19 dataset
+   :align: center
+
+Using darkmode and some custom font choices:
+
+.. image:: examples/plot_arxiv_ml.png
+   :width: 1024
+   :alt: A data map plot of papers from ArXiv ML
+   :align: center
+
+Alternative custom styling:
+
+.. image:: examples/plot_wikipedia.png
+   :width: 1024
+   :alt: A data map plot of Simple Wikipedia
+   :align: center
+
+Custom arrow styles, fonts, and colour maps:
+
+.. image:: examples/plot_simple_arxiv.png
+   :width: 1024
+   :alt: A styled data map plot of papers from ArXiv ML
+   :align: center
+
+------------
+Installation
+------------
+
+DataMapPlot requires a few libraries, but all are widely available and easy to install:
+
+ * Numpy
+ * Matplotlib
+ * Scikit-learn
+ * Pandas
+ * Datashader
+ * Scikit-image
+ * Numba
+
+To install DataMapPlot you can use pip:
+
+.. code:: bash
+
+    pip install datamapplot
+
+or use conda with conda-forge
+
+.. code:: bash
+
+    conda install -c conda-forge datamapplot
+
+
+-------
+License
+-------
+
+fast_hdbscan is MIT licensed. See the LICENSE file for details.
+
+------------
+Contributing
+------------
+
+Contributions are more than welcome! If you have ideas for features of projects please get in touch. Everything from
+code to notebooks to examples and documentation are all *equally valuable* so please don't feel you can't contribute.
+To contribute please `fork the project <https://github.com/TutteInstitute/datamapplot/issues#fork-destination-box>`_ make your
+changes and submit a pull request. We will do our best to work through any issues with you and get your code merged in.

doc/index.rst

@@ -11,11 +11,11 @@
 DataMapPlot: Creating beautiful plot of data maps
 =================================================
 
-DataMapPlot is a small library designed to help you make beautiful data map plots for
-inclusion in presentations, posters and papers. The focus is on producing static plots
-that are great looking with as little work for you as possible. While this involves
-automating most of the aesthetic choices, the library provides a wide variety of ways
-to customize the resulting plot to your needs.
+Creating beautiful plots of data maps. DataMapPlot is a small library designed to help you make beautiful data map
+plots for inclusion in presentations, posters and papers. The focus is on producing static plots that are great
+looking with as little work for you as possible. All you need to do is label clusters of points in the data map and
+DataMapPlot will take care of the rest. While this involves automating most of the aesthetic choices, the library
+provides a wide variety of ways to customize the resulting plot to your needs.
 
 Installation
 ------------

examples/plot_cord19.py

@@ -9,12 +9,19 @@
 import requests
 import PIL
 import matplotlib.pyplot as plt
+import pandas as pd
 
 plt.rcParams['savefig.bbox'] = 'tight'
 
 cord19_data_map = np.load("CORD19-subset-data-map.npy")
 cord19_labels = np.load("CORD19-subset-cluster_labels.npy", allow_pickle=True)
 
+# Prune labels down slightly
+label_counts = pd.Series(cord19_labels).value_counts()
+small_clusters = label_counts[label_counts <= 700].index
+for label in small_clusters:
+    cord19_labels[cord19_labels == label] = "Unlabelled"
+
 allenai_logo_response = requests.get(
     "https://allenai.org/newsletters/archive/2023-03-newsletter_files/927c3ca8-6c75-862c-ee5d-81703ef10a8d.png",
     stream=True,
@@ -30,12 +37,12 @@
     highlight_labels=[
         "Effects of the COVID-19 pandemic on mental health",
         "Airborne Transmission of COVID19",
-        "Diagnostic Testing for SARS-CoV2",
+        "COVID19 Diagnosis",
         "Viral Diseases and Emerging Zoonoses",
         "Vaccine Acceptance",
     ],
     label_font_size=6,
-    label_margin_factor=1.75,
+    label_margin_factor=1.5,
     label_direction_bias=1.0,
     highlight_label_keywords={"fontsize": 12, "fontweight": "bold", "bbox": {"boxstyle": "circle", "pad": 0.75}},
     logo=allenai_logo,