Annotated Heatmaps in Python

How to make Annotated Heatmaps in Python with Plotly.


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Annotated Heatmaps with Plotly Express

New in v5.5

As of version 5.5.0 of plotly, the recommended way to display annotated heatmaps is to use px.imshow() rather than the now-deprecated create_annotated_heatmap figure factory documented below for historical reasons.

Basic Annotated Heatmap for z-annotations

New in v5.5

After creating a figure with px.imshow, you can add z-annotations with .update_traces(texttemplate="%{z}").

In [1]:
import plotly.express as px

z = [[.1, .3, .5, .7, .9],
     [1, .8, .6, .4, .2],
     [.2, 0, .5, .7, .9],
     [.9, .8, .4, .2, 0],
     [.3, .4, .5, .7, 1]]

fig = px.imshow(z, text_auto=True)
fig.show()

Deprecated Figure Factory

The remaining examples show how to create Annotated Heatmaps with the deprecated create_annotated_heatmap figure factory.

Simple Annotated Heatmap

In [2]:
import plotly.figure_factory as ff

z = [[.1, .3, .5, .7, .9],
     [1, .8, .6, .4, .2],
     [.2, 0, .5, .7, .9],
     [.9, .8, .4, .2, 0],
     [.3, .4, .5, .7, 1]]

fig = ff.create_annotated_heatmap(z)
fig.show()

Custom Text and X & Y Labels

set annotation_text to a matrix with the same dimensions as z

WARNING: this legacy figure factory requires the y array to be provided in reverse order, and will map the z_text to the z values in reverse order. The use of the px.imshow() version below is highly recommended

In [3]:
import plotly.figure_factory as ff

z = [[.1, .3, .5],
     [1.0, .8, .6],
     [.6, .4, .2]]

x = ['Team A', 'Team B', 'Team C']
y = ['Game Three', 'Game Two', 'Game One']

z_text = [['Win', 'Lose', 'Win'],
          ['Lose', 'Lose', 'Win'],
          ['Win', 'Win', 'Lose']]

fig = ff.create_annotated_heatmap(z, x=x, y=y, annotation_text=z_text, colorscale='Viridis')
fig.show()

Here is the same figure using px.imshow()

In [4]:
import plotly.express as px

x = ['Team A', 'Team B', 'Team C']
y = ['Game One', 'Game Two', 'Game Three']

z = [[.1, .3, .5],
     [1.0, .8, .6],
     [.6, .4, .2]]

z_text = [['Win', 'Lose', 'Win'],
          ['Lose', 'Lose', 'Win'],
          ['Win', 'Win', 'Lose']]

fig = px.imshow(z, x=x, y=y, color_continuous_scale='Viridis', aspect="auto")
fig.update_traces(text=z_text, texttemplate="%{text}")
fig.update_xaxes(side="top")
fig.show()

Annotated Heatmap with numpy

In [5]:
import plotly.figure_factory as ff
import numpy as np
np.random.seed(1)

z = np.random.randn(20, 20)
z_text = np.around(z, decimals=2) # Only show rounded value (full value on hover)

fig = ff.create_annotated_heatmap(z, annotation_text=z_text, colorscale='Greys',
                                  hoverinfo='z')

# Make text size smaller
for i in range(len(fig.layout.annotations)):
    fig.layout.annotations[i].font.size = 8

fig.show()

Here is the same figure using px.imshow()

In [6]:
import plotly.express as px
import numpy as np
np.random.seed(1)

z = np.random.randn(20, 20)

fig = px.imshow(z, text_auto=".2f", color_continuous_scale='Greys', aspect="auto")
fig.show()

Here is a fairly contrived example showing how one can display a periodic table with custom text and hover using ff.create_annotated_heatmap() (scroll below to see the px.imshow() equivalent).

In [7]:
# Periodic Table Data
symbol = [['H', '', '', '', '', '', '', '', '', '', '', '', '', '', '', '', '', 'He'],
         ['Li', 'Be', '', '', '', '', '', '', '', '', '', '', 'B', 'C', 'N', 'O', 'F', 'Ne'],
         ['Na', 'Mg', '', '', '', '', '', '', '', '', '', '', 'Al', 'Si', 'P', 'S', 'Cl', 'Ar'],
         ['K', 'Ca', 'Sc', 'Ti', 'V', 'Cr', 'Mn', 'Fe', 'Co', 'Ni', 'Cu', 'Zn', 'Ga', 'Ge', 'As', 'Se', 'Br', 'Kr'],
         ['Rb ', 'Sr', 'Y', 'Zr', 'Nb', 'Mo', 'Tc', 'Ru', 'Rh', 'Pd', 'Ag', 'Cd', 'In', 'Sn', 'Sb', 'Te', 'I', 'Xe' ],
         ['Cs', 'Ba', '', 'Hf', 'Ta', 'W', 'Re', 'Os', 'Ir', 'Pt', 'Au', 'Hg', 'Tl', 'Pb', 'Bi', 'Po', 'At', 'Rn' ],
         ['Fr', 'Ra', '', 'Rf', 'Db', 'Sg', 'Bh', 'Hs', 'Mt', 'Ds', 'Rg', 'Cn', 'Uut', 'Fl', 'Uup', 'Lv', 'Uus', 'Uuo'],
         ['', '', 'La', 'Ce', 'Pr', 'Nd', 'Pm', 'Sm', 'Eu', 'Gd', 'Tb', 'Dy', 'Ho', 'Er', 'Tm', 'Yb', 'Lu', ''],
         ['', '', 'Ac', 'Th', 'Pa', 'U', 'Np', 'Pu', 'Am', 'Cm', 'Bk', 'Cf', 'Es', 'Fm', 'Md', 'No', 'Lr', '' ],
         ['', '', '', '', '', '', '', '', '', '', '', '', '', '', '', '', '', ''],
         ['', 'Alkali Metal', '', '', 'Transition Metal', '', '', 'Actinide', '', '', 'Semimetal', '', '', 'Halogen', '', '', '', ''],
         ['', 'Alkaline Metal', '', '', 'Lanthanide', '', '', 'Basic Metal', '', '', 'Nonmetal', '', '', 'Noble Gas', '', '', '', '']]

element = [['Hydrogen', '', '', '', '', '', '', '', '', '', '', '', '', '', '', '', '', 'Helium'],
           ['Lithium', 'Beryllium', '', '', '', '', '', '', '', '', '', '', 'Boron', 'Carbon', 'Nitrogen', 'Oxygen', 'Fluorine', 'Neon'],
           ['Sodium', 'Magnesium', '', '', '', '', '', '', '', '', '', '', 'Aluminium', 'Silicon', 'Phosphorus', 'Sulfur', 'Chlorine', 'Argon'],
           ['Potassium', 'Calcium', 'Scandium', 'Titanium', 'Vanadium', 'Chromium',  'Manganese', 'Iron', 'Cobalt', 'Nickel', 'Copper', 'Zinc', 'Gallium', 'Germanium', 'Arsenic', 'Selenium', 'Bromine', 'Krypton'],
           ['Rubidium', 'Strontium', 'Yttrium', 'Zirconium', 'Niobium', 'Molybdenum', 'Technetium', 'Ruthenium', 'Rhodium', 'Palladium', 'Silver', 'Cadmium', 'Indium', 'Tin', 'Antimony', 'Tellurium', 'Iodine', 'Xenon'],
           ['Cesium', 'Barium', '',  'Hafnium', 'Tantalum', 'Tungsten', 'Rhenium', 'Osmium', 'Iridium', 'Platinum', 'Gold', 'Mercury', 'Thallium', 'Lead', 'Bismuth', 'Polonium', 'Astatine', 'Radon'],
           ['Francium', 'Radium', '', 'Rutherfordium','Dubnium','Seaborgium','Bohrium','Hassium','Meitnerium','Darmstadtium','Roentgenium','Copernicium','Ununtrium','Ununquadium','Ununpentium','Ununhexium','Ununseptium','Ununoctium'],
           ['', '',  'Lanthanum', 'Cerium', 'Praseodymium', 'Neodymium', 'Promethium', 'Samarium', 'Europium', 'Gadolinium', 'Terbium', 'Dysprosium', 'Holmium', 'Erbium', 'Thulium', 'Ytterbium', 'Lutetium', ''],
           ['', '', 'Actinium', 'Thorium', 'Protactinium', 'Uranium', 'Neptunium', 'Plutonium', 'Americium', 'Curium', 'Berkelium', 'Californium', 'Einsteinium','Fermium' ,'Mendelevium', 'Nobelium', 'Lawrencium', '' ],
           ['', '', '', '', '', '', '', '', '', '', '', '', '', '', '', '', '', ''],
           ['', '', '', '', '', '', '', '', '', '', '', '', '', '', '', '', '', ''],
           ['', '', '', '', '', '', '', '', '', '', '', '', '', '', '', '', '', '']]

atomic_mass = [[ 1.00794, .0, .0, .0, .0, .0, .0, .0, .0, .0, .0, .0, .0, .0, .0, .0, .0,  4.002602],
     [ 6.941, 9.012182, .0, .0, .0, .0, .0, .0, .0, .0, .0, .0,  10.811, 12.0107, 14.0067, 15.9994, 18.9984032, 20.1797],
     [ 22.98976928, 24.3050, .0, .0, .0, .0, .0, .0, .0, .0, .0, .0,  26.9815386, 28.0855, 30.973762, 32.065, 35.453, 39.948],
     [ 39.0983, 40.078, 44.955912, 47.867, 50.9415, 51.9961, 54.938045, 55.845, 58.933195, 58.6934, 63.546, 65.38, 69.723, 72.64, 74.92160, 78.96, 79.904, 83.798],
     [ 85.4678, 87.62, 88.90585, 91.224, 92.90638, 95.96, 98, 101.07, 102.90550, 106.42, 107.8682, 112.411, 114.818, 118.710, 121.760, 127.60, 126.90447, 131.293],
     [ 132.9054519, 137.327, .0, 178.49, 180.94788, 183.84, 186.207, 190.23, 192.217, 195.084, 196.966569, 200.59, 204.3833, 207.2, 208.98040, 209, 210, 222],
     [223, 226, .0, 267, 268, 271, 272, 270, 276, 281, 280, 285, 284, 289, 288, 293, 'unknown', 294],
     [.0, .0, 138.90547, 140.116, 140.90765, 144.242, 145, 150.36, 151.964, 157.25, 158.92535, 162.500, 164.93032, 167.259, 168.93421, 173.054, 174.9668, .0],
     [.0, .0, 227, 232.03806, 231.03588, 238.02891, 237, 244, 243, 247, 247, 251, 252, 257, 258, 259, 262, .0],
     [.0, .0, .0, .0, .0, .0, .0, .0, .0, .0, .0, .0, .0, .0, .0, .0, .0, .0],
     [.0, .0, .0, .0, .0, .0, .0, .0, .0, .0, .0, .0, .0, .0, .0, .0, .0, .0],
     [.0, .0, .0, .0, .0, .0, .0, .0, .0, .0, .0, .0, .0, .0, .0, .0, .0, .0]]

color = [[.8, .0, .0, .0, .0, .0, .0, .0, .0, .0, .0, .0, .0, .0, .0, .0, .0, 1.],
     [.1, .2, .0, .0, .0, .0, .0, .0, .0, .0, .0, .0, .7, .8, .8, .8, .9, 1.],
     [.1, .2, .0, .0, .0, .0, .0, .0, .0, .0, .0, .0, .6, .7, .8, .8, .9, 1],
     [.1, .2, .3, .3, .3, .3, .3, .3, .3, .3, .3, .3, .6, .7, .8, .8, .9, 1.],
     [.1, .2, .3, .3, .3, .3, .3, .3, .3, .3, .3, .3, .6, .6, .7, .7, .9, 1.],
     [.1, .2, .4, .3, .3, .3, .3, .3, .3, .3, .3, .3, .6, .6, .6, .7, .9, 1.],
     [.1, .2, .5, .3, .3, .3, .3, .3, .3, .3, .3, .3, .6, .6, .6, .6, .9, 1.],
     [.0, .0, .4, .4, .4, .4, .4, .4, .4, .4, .4, .4, .4, .4, .4, .4, .4, .0],
     [.0, .0, .5, .5, .5, .5, .5, .5, .5, .5, .5, .5, .5, .5, .5, .5, .5, .0],
     [.0, .0, .0, .0, .0, .0, .0, .0, .0, .0, .0, .0, .0, .0, .0, .0, .0, .0],
     [.1, .1, .1, .3, .3, .3, .5, .5, .5, .7, .7, .7, .9, .9, .9, .0, .0, .0],
     [.2, .2, .2, .4, .4, .4, .6, .6, .6, .8, .8, .8, 1., 1., 1., .0, .0, .0]]

# Set Colorscale
colorscale=[[0.0, 'rgb(255,255,255)'], [.2, 'rgb(255, 255, 153)'],
            [.4, 'rgb(153, 255, 204)'], [.6, 'rgb(179, 217, 255)'],
            [.8, 'rgb(240, 179, 255)'],[1.0, 'rgb(255, 77, 148)']]

# Display element name and atomic mass on hover
hover=[]
for x in range(len(symbol)):
    hover.append([i + '<br>' + 'Atomic Mass: ' + str(j) if i else ''
                      for i, j in zip(element[x], atomic_mass[x])])

import plotly.figure_factory as ff
# Make Annotated Heatmap
fig = ff.create_annotated_heatmap(color[::-1], annotation_text=symbol[::-1], text=hover[::-1],
                                 colorscale=colorscale, font_colors=['black'], hoverinfo='text')
fig.update_layout(
     title_text='Periodic Table',
     margin=dict(l=10, r=10, t=10, b=10, pad=10),
     xaxis=dict(zeroline=False, showgrid=False),
     yaxis=dict(zeroline=False, showgrid=False, scaleanchor="x"),
)
fig.show()

Here is the same output using px.imshow() with much less array manipulation:

In [8]:
import plotly.express as px
import numpy as np

fig = px.imshow(color, color_continuous_scale=colorscale, aspect="auto",
               title='Periodic Table')
fig.update_traces(
    text=symbol, texttemplate="%{text}", textfont_size=12,
    customdata=np.moveaxis([element, atomic_mass], 0,-1),
    hovertemplate="%{customdata[0]}<br>Atomic Mass: %{customdata[1]:.2f}<extra></extra>"
)
fig.update_xaxes(visible=False)
fig.update_yaxes(visible=False)
fig.update_coloraxes(showscale=False)
fig.show()

Reference

For more info on Plotly heatmaps, see: https://plotly.com/python/reference/heatmap/.
For more info on using colorscales with Plotly see: https://plotly.com/python/heatmap-and-contour-colorscales/
For more info on ff.create_annotated_heatmap(), see the full function reference

What About Dash?

Dash is an open-source framework for building analytical applications, with no Javascript required, and it is tightly integrated with the Plotly graphing library.

Learn about how to install Dash at https://dash.plot.ly/installation.

Everywhere in this page that you see fig.show(), you can display the same figure in a Dash application by passing it to the figure argument of the Graph component from the built-in dash_core_components package like this:

import plotly.graph_objects as go # or plotly.express as px
fig = go.Figure() # or any Plotly Express function e.g. px.bar(...)
# fig.add_trace( ... )
# fig.update_layout( ... )

import dash
import dash_core_components as dcc
import dash_html_components as html

app = dash.Dash()
app.layout = html.Div([
    dcc.Graph(figure=fig)
])

app.run_server(debug=True, use_reloader=False)  # Turn off reloader if inside Jupyter