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Problem plotting a raster (GeoTIFF) on top of a basemap (Google Maps / Mapbox) with Python

I've been stuck for a few days trying to plot a TIF file over a basemap (Google Maps or Mapbox) using Python. I don't know if this is actually possible because I didn't find examples and nothing very clear about it, the most I found is how to plot vector files (shp) on top of basemaps, but nothing about raster.
I have a raster (rainfall_clipped.tif) that is in EPSG:4326 and I'm trying to plot it on top of a MapBox map using the Contextily package. At first I suspected that it could be a projection problem, but even doing the conversions to EPSG:3857, it didn't work. In the documentation Contextily says that it accepts both projections.
Contextily seems to understand the projections, even because it generates the map with the correct axes, the big problem is that it doesn't plot the TIF file on the map. And it's also reading the raster because it loaded the colorbar with the correct values. I don't know if the layer order is wrong or what else it could be.
Below is the code I am using and then the image that is being generated:
data = rasterio.open("rainfall_clipped.tif")
# Read the bounds
left, bottom, right, top = data.bounds
# Create a figure and axes
fig, ax = plt.subplots(figsize=(10, 10))
# Add the raster data to the plot using imshow
im = ax.imshow(data.read(1), extent=[left, right, bottom, top], cmap="Blues")
# Add a colorbar
fig.colorbar(im, ax=ax)
# Add a basemap using contextily
ctx.add_basemap(ax, crs=data.crs, source=ctx.providers.MapBox(accessToken="my_key", id="mapbox/satellite-v9"))
# Show the plot
plt.show()
This code is generating this image:
Output image
What I'm trying to do is something like below:
Expected image
Any suggestions what I can do?

Draw Basemap above xarray plot

I have a xarray dataset clip_ds and have visualised the data array using plot. Now, I want to add a country boundary using Basemap's drawcountries(). Apparently, there is something wrong with the extent I am using in basemap (I guess), but both the country border and the data plot won't show up together. I have tried interchanging the position of clip_ds.pr[0].plot() before and after I create basemap, and it gives me two different results as shown below:
Xarray PLOT BEFORE BASEMAP (Note that the colorbar from xarray plot is still there)
Xarray PLOT AFTER BASEMAP (Notice difference from 3, height of the plot shrinks here and the tick labels disappears, probably overlapped by basemap.)
Xarray plot only
Loading seperate shapefile using map.readshapefile also gives same kind of problem. I know there might be a way around this using cartopy, but I like the Basemap functionalities and would like to know if there is any solution to this.
map=Basemap(projection='merc',
resolution='l',
llcrnrlon=clip_ds.lon[0],
llcrnrlat=clip_ds.lat[0],
urcrnrlon=clip_ds.lon[-1],
urcrnrlat=clip_ds.lat[-1])
map.drawcountries()
clip_ds.pr[0].plot()
plt.show()

Changing center of rotation in a Matplotlib 3D plot

I have a 3D line plot in matplotlib, created using the following code:
def view(self):
from mpl_toolkits.mplot3d import Axes3D #noqa
import matplotlib.pyplot as plt
ax = plt.figure().gca(projection='3d')
history = np.array(self.position_history)
x, y ,z = history[:, 0], history[:, 1], history[:, 2]
ax.plot(x, y, z)
plt.show()
Here history is an Mx3 array of points. This works fine and pops up a plot as expected. I am able to click and drag to modify the azimuth and elevation interactively. I am able to zoom by right-clicking and dragging.
However I am wondering if it is possible to modify the center point of the pan and zoom? I would like to zoom into the top-right, and then pan around with the top right as my center of rotation. If you have ever used solidworks or another CAD program, this is the behavior I am after. Is this doable? If not interactively, can I do it programmatically?
And finally, if none of this is possible in matplotlib, is there another library that can accomplish what I want?

I have also run into trouble in the past in terms of customizing mplot3d, rather unsuccessfully..
And finally, if none of this is possible in matplotlib, is there another library that can accomplish what I want?
you can do this with mayavi
here is a relevant stackoverflow answer for customizing how you interact with your plot
there are also various useful tips and tricks for animating in general and for using mayavi
(apologies if this isn't useful)

Not sure this will do what you need but you can define the center when you first plot. Here, "c_x" is the center of rotation on the x axis and the -/+ 200 defines the axis to be 200 units in both direction. Likewise for y and z.
If you had the user choose the center before plotting, that could work as a crude work around.
http://matplotlib.org/api/axes_api.html?highlight=set_xbound#matplotlib.axes.Axes.set_xbound
fig = plt.figure()
ax = fig.add_subplot(111, projection='3d')
ax.autoscale(enable=False,axis='both') #you will need this line to change the Z-axis
ax.set_xbound(c_x-200, c_x+200)
ax.set_ybound(c_y-200, c_y+200)
ax.set_zbound(c_z-200, c_z+200)

Plotting points in python

I want to plot some (x,y) points on the same graph and I don't need any special features at all short of support for polar coordinates which would be nice but not necessary. It's mostly for visualizing my data. Is there a simple way to do this? Matplotlib seems like way more than I need right now. Are there any more basic modules available? What do You recommend?

Go with matplotlib Chance is that sometime in the future you might need to do more than just "simple" stuff and then you don't need to invest time learning a new plot-tool.
See this link for list of plotting tools for python...

Absolutely. Matplotlib is the way to go.
The pyplot module provides a nice interface to get simple plots up and running fast, especially if you are familiar with MatLab's plotting environment. Here is a simple example using pyplot:
import matplotlib.pyplot as plt
fig = plt.figure()
ax = fig.add_subplot(111)
x_points = xrange(0,9)
y_points = xrange(0,9)
p = ax.plot(x_points, y_points, 'b')
ax.set_xlabel('x-points')
ax.set_ylabel('y-points')
ax.set_title('Simple XY point plot')
fig.show()

import matplotlib.pyplot as plt
x = range(1,10)
y = range(1,10)
plt.plot(x,y,'o')
plt.show()
Here's a simple line with made up x, y. Note: x and y are lists.
Their lengths should be equal or you'll get a error. Cheers!

I suggest the most good looking plotting library for Python: CairoPlot

You can use the Tkinter canvas widget. It uses rectangular coordinates but of course you can translate to polar. The canvas is pretty much just like it sounds -- a blank canvas on which you can draw points, lines, circles, rectangles, etc.

You could always write a plotting function that uses the turtle module from the standard library.

MathGL is GPL plotting library which have Python interface, arbitrary (including polar) curved coordinates, a lot of plot types, export to PNG, EPS, SVG, widgets, and so on. For 1D plot samples see here.

Have you tried to use pillow?
from PIL import Image, ImageDraw
#Set up canvas
img = Image.new (mode, size)
draw = ImageDraw.Draw (img)
#Draw your points
draw.point (xy, colour)

How to draw floating pie charts on an existing plot with matplotlib

I would like to plot multiple pie charts over an existing plot using absolute coordinates.
I went through the add_axes method and also the AxesGrid toolikt but couldn't find a solution.
To be more specific, I want to draw pie charts over a geographical map using the basemap module.

This tutorial explains how to use matplotlib Basemap for drawing pie charts on a map. It is fairly simple and gives code examples.