Commit 00d179f7 authored by Sean Fitzgibbon's avatar Sean Fitzgibbon
Browse files

Added first pass at plotly examples notebook

parent d0d5b224
%% Cell type:markdown id: tags:
# `plotly.py`
[`plotly.py`](https://plotly.com/python/) a python interface to the `plotly` javascript library which is an open-source graphing library which specialises in high-quality web-based interactive graphs. `plotly.py` allows you to create these interactive web-based plots without having to code in javascript.
`plotly.py` has excellent documentation: https://plotly.com/python/
This notebook is not intended to instruct you how to use `plotly.py`. Instead it pulls together interesting examples from the `plotly.py` documentation into a single notebook to give you a taster of what can be done with `plotly.py`.
## Install `plotly.py`
`plotly` is not installed in the `fslpython` environment so you will need to install it to run this notebook. In a terminal run the following command (you will need admin privileges):
```
sudo $FSLDIR/fslpython/bin/conda install -c conda-forge -n fslpython plotly
```
## Line & Scatter Plots
https://plotly.com/python/line-and-scatter/
%% Cell type:code id: tags:
``` python
import plotly.graph_objects as go
# Create random data with numpy
import numpy as np
np.random.seed(1)
N = 100
random_x = np.linspace(0, 1, N)
random_y0 = np.random.randn(N) + 5
random_y1 = np.random.randn(N)
random_y2 = np.random.randn(N) - 5
fig = go.Figure()
# Add traces
fig.add_trace(go.Scatter(x=random_x, y=random_y0,
mode='markers',
name='markers'))
fig.add_trace(go.Scatter(x=random_x, y=random_y1,
mode='lines+markers',
name='lines+markers'))
fig.add_trace(go.Scatter(x=random_x, y=random_y2,
mode='lines',
name='lines'))
fig.show()
```
%% Cell type:markdown id: tags:
## Bar Charts
https://plotly.com/python/bar-charts/
%% Cell type:code id: tags:
``` python
import plotly.graph_objects as go
months = ['Jan', 'Feb', 'Mar', 'Apr', 'May', 'Jun',
'Jul', 'Aug', 'Sep', 'Oct', 'Nov', 'Dec']
fig = go.Figure()
fig.add_trace(go.Bar(
x=months,
y=[20, 14, 25, 16, 18, 22, 19, 15, 12, 16, 14, 17],
name='Primary Product',
marker_color='indianred'
))
fig.add_trace(go.Bar(
x=months,
y=[19, 14, 22, 14, 16, 19, 15, 14, 10, 12, 12, 16],
name='Secondary Product',
marker_color='lightsalmon'
))
# Here we modify the tickangle of the xaxis, resulting in rotated labels.
fig.update_layout(barmode='group', xaxis_tickangle=-45)
fig.show()
```
%% Cell type:markdown id: tags:
## Box Plots
https://plotly.com/python/box-plots/
%% Cell type:code id: tags:
``` python
import plotly.express as px
df = px.data.tips()
fig = px.box(df, x="day", y="total_bill", color="smoker")
fig.update_traces(quartilemethod="exclusive") # or "inclusive", or "linear" by default
fig.show()
```
%% Cell type:markdown id: tags:
## Distribution Plots
https://plotly.com/python/distplot/
%% Cell type:code id: tags:
``` python
import plotly.figure_factory as ff
import numpy as np
# Add histogram data
x1 = np.random.randn(200) - 2
x2 = np.random.randn(200)
x3 = np.random.randn(200) + 2
x4 = np.random.randn(200) + 4
# Group data together
hist_data = [x1, x2, x3, x4]
group_labels = ['Group 1', 'Group 2', 'Group 3', 'Group 4']
# Create distplot with custom bin_size
fig = ff.create_distplot(hist_data, group_labels, bin_size=.2)
fig.show()
```
%% Cell type:markdown id: tags:
## Violin Plots
https://plotly.com/python/violin/
%% Cell type:code id: tags:
``` python
import plotly.graph_objects as go
import pandas as pd
df = pd.read_csv("https://raw.githubusercontent.com/plotly/datasets/master/violin_data.csv")
fig = go.Figure()
days = ['Thur', 'Fri', 'Sat', 'Sun']
for day in days:
fig.add_trace(go.Violin(x=df['day'][df['day'] == day],
y=df['total_bill'][df['day'] == day],
name=day,
box_visible=True,
meanline_visible=True))
fig.show()
```
%% Cell type:markdown id: tags:
## Dendrogram with Heatmap
https://plotly.com/python/dendrogram/
%% Cell type:code id: tags:
``` python
import plotly.graph_objects as go
import plotly.figure_factory as ff
import numpy as np
from scipy.spatial.distance import pdist, squareform
# get data
data = np.genfromtxt("http://files.figshare.com/2133304/ExpRawData_E_TABM_84_A_AFFY_44.tab",
names=True,usecols=tuple(range(1,30)),dtype=float, delimiter="\t")
data_array = data.view((float, len(data.dtype.names)))
data_array = data_array.transpose()
labels = data.dtype.names
# Initialize figure by creating upper dendrogram
fig = ff.create_dendrogram(data_array, orientation='bottom', labels=labels)
for i in range(len(fig['data'])):
fig['data'][i]['yaxis'] = 'y2'
# Create Side Dendrogram
dendro_side = ff.create_dendrogram(data_array, orientation='right')
for i in range(len(dendro_side['data'])):
dendro_side['data'][i]['xaxis'] = 'x2'
# Add Side Dendrogram Data to Figure
for data in dendro_side['data']:
fig.add_trace(data)
# Create Heatmap
dendro_leaves = dendro_side['layout']['yaxis']['ticktext']
dendro_leaves = list(map(int, dendro_leaves))
data_dist = pdist(data_array)
heat_data = squareform(data_dist)
heat_data = heat_data[dendro_leaves,:]
heat_data = heat_data[:,dendro_leaves]
heatmap = [
go.Heatmap(
x = dendro_leaves,
y = dendro_leaves,
z = heat_data,
colorscale = 'Blues'
)
]
heatmap[0]['x'] = fig['layout']['xaxis']['tickvals']
heatmap[0]['y'] = dendro_side['layout']['yaxis']['tickvals']
# Add Heatmap Data to Figure
for data in heatmap:
fig.add_trace(data)
# Edit Layout
fig.update_layout({'width':800, 'height':800,
'showlegend':False, 'hovermode': 'closest',
})
# Edit xaxis
fig.update_layout(xaxis={'domain': [.15, 1],
'mirror': False,
'showgrid': False,
'showline': False,
'zeroline': False,
'ticks':""})
# Edit xaxis2
fig.update_layout(xaxis2={'domain': [0, .15],
'mirror': False,
'showgrid': False,
'showline': False,
'zeroline': False,
'showticklabels': False,
'ticks':""})
# Edit yaxis
fig.update_layout(yaxis={'domain': [0, .85],
'mirror': False,
'showgrid': False,
'showline': False,
'zeroline': False,
'showticklabels': False,
'ticks': ""
})
# Edit yaxis2
fig.update_layout(yaxis2={'domain':[.825, .975],
'mirror': False,
'showgrid': False,
'showline': False,
'zeroline': False,
'showticklabels': False,
'ticks':""})
# Plot!
fig.show()
```
%% Cell type:markdown id: tags:
## Network Graph
https://plotly.com/python/network-graphs/
%% Cell type:code id: tags:
``` python
import plotly.graph_objects as go
import networkx as nx
G = nx.random_geometric_graph(200, 0.125)
edge_x = []
edge_y = []
for edge in G.edges():
x0, y0 = G.nodes[edge[0]]['pos']
x1, y1 = G.nodes[edge[1]]['pos']
edge_x.append(x0)
edge_x.append(x1)
edge_x.append(None)
edge_y.append(y0)
edge_y.append(y1)
edge_y.append(None)
edge_trace = go.Scatter(
x=edge_x, y=edge_y,
line=dict(width=0.5, color='#888'),
hoverinfo='none',
mode='lines')
node_x = []
node_y = []
for node in G.nodes():
x, y = G.nodes[node]['pos']
node_x.append(x)
node_y.append(y)
node_trace = go.Scatter(
x=node_x, y=node_y,
mode='markers',
hoverinfo='text',
marker=dict(
showscale=True,
# colorscale options
#'Greys' | 'YlGnBu' | 'Greens' | 'YlOrRd' | 'Bluered' | 'RdBu' |
#'Reds' | 'Blues' | 'Picnic' | 'Rainbow' | 'Portland' | 'Jet' |
#'Hot' | 'Blackbody' | 'Earth' | 'Electric' | 'Viridis' |
colorscale='YlGnBu',
reversescale=True,
color=[],
size=10,
colorbar=dict(
thickness=15,
title='Node Connections',
xanchor='left',
titleside='right'
),
line_width=2))
node_adjacencies = []
node_text = []
for node, adjacencies in enumerate(G.adjacency()):
node_adjacencies.append(len(adjacencies[1]))
node_text.append('# of connections: '+str(len(adjacencies[1])))
node_trace.marker.color = node_adjacencies
node_trace.text = node_text
fig = go.Figure(data=[edge_trace, node_trace],
layout=go.Layout(
titlefont_size=16,
showlegend=False,
hovermode='closest',
margin=dict(b=20,l=5,r=5,t=40),
xaxis=dict(showgrid=False, zeroline=False, showticklabels=False),
yaxis=dict(showgrid=False, zeroline=False, showticklabels=False))
)
fig.show()
```
%% Cell type:markdown id: tags:
## Custom Controls: Sliders
https://plotly.com/python/sliders/
%% Cell type:code id: tags:
``` python
import plotly.graph_objects as go
import numpy as np
# Create figure
fig = go.Figure()
# Add traces, one for each slider step
for step in np.arange(0, 5, 0.1):
fig.add_trace(
go.Scatter(
visible=False,
line=dict(color="#00CED1", width=6),
name="𝜈 = " + str(step),
x=np.arange(0, 10, 0.01),
y=np.sin(step * np.arange(0, 10, 0.01))))
# Make 10th trace visible
fig.data[10].visible = True
# Create and add slider
steps = []
for i in range(len(fig.data)):
step = dict(
method="update",
args=[{"visible": [False] * len(fig.data)},
{"title": "Slider switched to step: " + str(i)}], # layout attribute
)
step["args"][0]["visible"][i] = True # Toggle i'th trace to "visible"
steps.append(step)
sliders = [dict(
active=10,
currentvalue={"prefix": "Frequency: "},
pad={"t": 50},
steps=steps
)]
fig.update_layout(
sliders=sliders
)
fig.show()
```
%% Cell type:markdown id: tags:
## Custom Controls: Dropdown Menus
https://plotly.com/python/dropdowns/
%% Cell type:code id: tags:
``` python
import plotly.graph_objects as go
import pandas as pd
# load dataset
df = pd.read_csv("https://raw.githubusercontent.com/plotly/datasets/master/volcano.csv")
# Create figure
fig = go.Figure()
# Add surface trace
fig.add_trace(go.Heatmap(z=df.values.tolist(), colorscale="Viridis"))
# Update plot sizing
fig.update_layout(
width=800,
height=900,
autosize=False,
margin=dict(t=100, b=0, l=0, r=0),
)
# Update 3D scene options
fig.update_scenes(
aspectratio=dict(x=1, y=1, z=0.7),
aspectmode="manual"
)
# Add dropdowns
button_layer_1_height = 1.08
fig.update_layout(
updatemenus=[
dict(
buttons=list([
dict(
args=["colorscale", "Viridis"],
label="Viridis",
method="restyle"
),
dict(
args=["colorscale", "Cividis"],
label="Cividis",
method="restyle"
),
dict(
args=["colorscale", "Blues"],
label="Blues",
method="restyle"
),
dict(
args=["colorscale", "Greens"],
label="Greens",
method="restyle"
),
]),
direction="down",
pad={"r": 10, "t": 10},
showactive=True,
x=0.1,
xanchor="left",
y=button_layer_1_height,
yanchor="top"
),
dict(
buttons=list([
dict(
args=["reversescale", False],
label="False",
method="restyle"
),
dict(
args=["reversescale", True],
label="True",
method="restyle"
)
]),
direction="down",
pad={"r": 10, "t": 10},
showactive=True,
x=0.37,
xanchor="left",
y=button_layer_1_height,
yanchor="top"
),
dict(
buttons=list([
dict(
args=[{"contours.showlines": False, "type": "contour"}],
label="Hide lines",
method="restyle"
),
dict(
args=[{"contours.showlines": True, "type": "contour"}],
label="Show lines",
method="restyle"
),
]),
direction="down",
pad={"r": 10, "t": 10},
showactive=True,
x=0.58,
xanchor="left",
y=button_layer_1_height,
yanchor="top"
),
]
)
fig.update_layout(
annotations=[
dict(text="colorscale", x=0, xref="paper", y=1.06, yref="paper",
align="left", showarrow=False),
dict(text="Reverse<br>Colorscale", x=0.25, xref="paper", y=1.07,
yref="paper", showarrow=False),
dict(text="Lines", x=0.54, xref="paper", y=1.06, yref="paper",
showarrow=False)
])
fig.show()
```
%% Cell type:code id: tags:
``` python
```
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