python - Some values of matrix do not appear in the plot by Matplotlib -


i created empty reference matrix csv, located (x,y) position on matrix (and printed them out), , designated 100 position on matrix. each x value in ref_mass pandas series.

ref_df = pd.read_csv(ref_file) reference = np.zeros(shape=(1201,len(ref_df))) ref_mass = ref_df["mass"]  i, mass in enumerate(ref_mass):   print ref_mass[i].astype(int) - 300, # print (x,y)   reference[(ref_mass[i].astype(int) - 300),i] = 100

every (x,y) printed out correctly. however, there no value in plot of (x,y). what's wrong here? checked reference matrix, has 100 in every column rightly.

the (x,y): 

547 0 265 1 124 2 39 3 509 4 # shown 240 5 # shown 105 6 24 7 355 8 137 9 28 10 # shown 394 11 163 12 48 13 347 14 132 15 # shown 24 16

the plot: enter image description here

plot code:

if __name__ == '__main__':   mpl_toolkits.mplot3d import axes3d   import matplotlib.pyplot plt   import matplotlib   matplotlib.matplotlib_fname()    plt.ylabel('m/z')   plt.xlabel('peptides')    plt.imshow(reference, aspect='auto', cmap='terrain')   plt.colorbar()   plt.tight_layout()    plt.show()

every pixel in final image represents 3 or more data points. renderer has decide color out of 2 times blue, 1 time white map pixel. statistically, blue twice white, such 66% of data points not shown.

the number of 3 pixels comes rough calculation: image has 480 pixels (which can either find out in picture program or calculating figuresize*dpi). have 1200 datapoints (seen axes). have margin of ~10% @ both ends; have 1200/(0.8*480) = 3.1 datapoints per pixel in final image.

imshow interpolation

you can use interpolation on image make pixels appear, e.g.

plt.imshow(..., interpolation="sinc")

the result may not appealing visually.

change resolution

you can make sure final plot comprises 1 pixel per datapoint. i.e. 1200 pixels dpi of 100 can do

m = 0.1 plt.figure(figsize=(8, (1+2.*m)*1200./dpi )) plt.subplots_adjust(bottom=m, top=1.-m) plt.imshow(...)

filter data

another option change data, such 1 pixel becomes 3 pixels along y direction.

import matplotlib.pyplot plt import numpy np; np.random.seed(1) import scipy.ndimage.filters filters  = np.zeros((1200, 16)) in range(16):     a[i*70+21, i] = 1  kernel = np.array([[0.,1.,0.],                    [0.,1.,0.],                    [0.,1.,0.]]) anew = filters.convolve(a,kernel,mode='constant', cval=0)  im = plt.imshow(anew, aspect="auto") plt.colorbar(im)  plt.show()

enter image description here

drawing lines

import matplotlib.pyplot plt import numpy np  = np.zeros((1200, 16))  im = plt.imshow(a, aspect="auto", vmin=0, vmax=1) plt.colorbar(im)  in range(16):     plt.plot([i-.5, i+.5], [i*70+21,i*70+21], color=im.cmap(1.))  plt.show()

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