plotly_fig['data'][i]['base'] = 'relative' where i is the index of each bar trace in your graph.
another problem I had was that
tls.mpl_to_plotly converted the negative numbers in the y axis to positive ones and I had to change them back manually. See my example code below. Even after setting base mode to relative the chart didn’t work and I needed to reset the y axis.
I’m sorry this is such a work-around.
import matplotlib.pyplot as plt
import plotly.offline as py
# Learn about API authentication here: https://plot.ly/python/getting-started
# Find your api_key here: https://plot.ly/settings/api
y = [3, 10, -7, 5, 3, 4.5, 6, 8.1]
N = len(y)
x = range(N)
width = 1/1.5
plt.bar(x, y, width, color="blue")
fig = plt.gcf()
plotly_fig = tls.mpl_to_plotly(fig)