I want to plot something like a biplot in python Plotly ,but using 3 principal components so as to make a 3d plot.
How do I go about plotting the direction vectors(the red lines) of principal components in plotly python?
There is exactly the same question , but for R, here. I am not able to translate the code perfectly.
With much help from here
from plotly.offline import plot
import plotly.graph_objs as go
pca = PCA(n_components=3).fit(iris.data)
X_reduced = pca.transform(iris.data)
trace1 = go.Scatter3d(
x=X_reduced[:,0],
y = X_reduced[:,1],
z = X_reduced[:,2],
mode='markers',
marker=dict(
size=12,
color= target,
opacity=1
)
)
dc_1 = go.Scatter3d( x = [0,pca.components_.T[0][0]],
y = [0,pca.components_.T[0][1]],
z = [0,pca.components_.T[0][2]],
marker = dict( size = 1,
color = "rgb(84,48,5)"),
line = dict( color = "red",
width = 6),
name = "Var1"
)
dc_2 = go.Scatter3d( x = [0,pca.components_.T[1][0]],
y = [0,pca.components_.T[1][1]],
z = [0,pca.components_.T[1][2]],
marker = dict( size = 1,
color = "rgb(84,48,5)"),
line = dict( color = "green",
width = 6),
name = "Var2"
)
dc_3 = go.Scatter3d( x = [0,pca.components_.T[2][0]],
y = [0,pca.components_.T[2][1]],
z = [0,pca.components_.T[2][2]],
marker = dict( size = 1,
color = "rgb(84,48,5)"),
line = dict( color = "blue",
width = 6),
name = "Var3"
)
dc_4 = go.Scatter3d( x = [0,pca.components_.T[3][0]],
y = [0,pca.components_.T[3][1]],
z = [0,pca.components_.T[3][2]],
marker = dict( size = 1,
color = "rgb(84,48,5)"),
line = dict( color = "yellow",
width = 6),
name = "Var4"
)
data = [trace1,dc_1,dc_2,dc_3,dc_4]
layout = go.Layout(
xaxis=dict(
title='PC1',
titlefont=dict(
family='Courier New, monospace',
size=18,
color='#7f7f7f'
)
)
)
fig = go.Figure(data=data, layout=layout)
plot(fig, filename='3d-scatter-tupac-with-mac')
from sklearn.decomposition import PCA and from sklearn.datasets import load_irisare requiredcolor= target should be color= iris.target