Awesome Open Source
Awesome Open Source

A Simple Tool for Ploting the Heatmap Overlay Image

Jupyter Notebook Demo

HeatMap Class: 3 inputs:

  1. image: image path (string) or image value (numpy array)
  2. heatmap: 2-D numpy value (no shape restriction)
  3. (optional) gaussian filter: mosaic smoothing (gaussian_std, default is 10. when set to 0, means no filter apply)
from HeatMap import HeatMap
# input a image path and a numpy array heatmap
hm = HeatMap('demo_image.jpg',heat_map)
# or input a numpy array image and heatmap
hm = HeatMap(image,heat_map,gaussian_std=0)

Method 1 plot: 6 parameters (all optional)

  1. transparency: define the transparency of heamap overlay (lower -> more transparent, default is 0.7)
  2. color_map: color map style (default is bwr)
  3. show_axis: show axis or not (boolean True/False, default is False)
  4. show_original: show original image (boolean True/False, default is False)
  5. show_colorbar: show color bar (boolean True/False, default is False)
  6. width_pad: the width padding (default is 0, set to negative value for reducing the space between figures)
#simple default plot
hm.plot()

#customised plot
hm.plot(transparency=0.6,
        color_map='seismic',
        show_axis=True,
        show_original=True,
        show_colorbar=True,
        width_pad=-10)

Method 2 save: 1 required, 8+ optional*

required

  1. filename: filename for saved figure (string)

optinal:

  1. save_path: figure saving directory (default is the current working directory)
  2. formate: figure saving fomate (jpg, jpeg, png, pdf, ps, eps and svg), default is 'png'
  3. transparency: define the transparency of heamap overlay (lower -> more transparent, default is 0.7)
  4. color_map: color map style (default is bwr)
  5. show_axis: show axis or not (boolean True/False, default is False)
  6. show_original: show original image (boolean True/False, default is False)
  7. show_colorbar: show color bar (boolean True/False, default is False)
  8. width_pad: the width padding (default is 0, set to negative value for reducing the space between figures)
  9. other parameters from pyplot.savefig can be used here
# simple save
hm.save('heatmap_result_1')
# customised save
hm.save('heatmap_result_2','png',
        transparency=0.6,
        color_map='seismic',
        show_axis=True,
        show_original=True,
        show_colorbar=True,
        width_pad=-10)

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Python (865,958
Boolean (8,256
Numpy (6,168
Overlay (4,889
Matplotlib (4,228
Heatmap (1,587