Y_axis ticks stacking when values are set in logarithmic plot

Question

I am trying to plot a scatter plot with a logarithmic y-axis (Like this but with the y-axis being logarithmic). I am able to get the plot to work properly before I change the y tick values, but as soon as I change the values to the ones I desire the plot ends up with the wrong scale. I am displaying the plot on a GUI made using tkinter. What am I missing? Any help would be greatly appreciated.

The code I am using:

    x=np.array (x_values)
    y= np.array (y_values)
    
    fig = Figure(figsize=(6,6))
    a = fig.add_subplot(111)
    a.scatter(x,y,color='red')
   
    a.set_title ("Estimation Grid", fontsize=16)
    a.set_ylabel("Y", fontsize=14)
    a.set_xlabel("X", fontsize=14)
    
    a.set_yscale("log")
    #a.set_yticks([100, 50, 10, 1.5, 1, 0.5, 0.1, 0.01, 0])
    a.set_yticks([0, 0.01, 0.1, 0.5, 1, 1.5, 10, 50, 100])
    a.get_yaxis().set_major_formatter(matplotlib.ticker.LogFormatter())
    a.grid()

The resulting plot:

The values used for this plot are:

x_values =[0.1, 0.2, 0.3, 0.4, 0.5, 0.6, 0.7, 0.8]

y_values = [99.99, 75, 60, 50, 45, 40, 35, 30]

Questions I've looked at: Overlapping axis tick labels in logarithmic plots set ticks with logarithmic scale

Don't include zero in your yticks for a log plot. As log(0) is minus infinity the distance between tick 0 and tick 0.01 will be much too large. You can choose another small but positive value for the smallest y, e.g. 0.0001, depending on your data. — JohanC
– JohanC, Commented May 19, 2020 at 16:05

BigBen · Accepted Answer · 2020-05-19 16:47:33Z

0

Don't include zero in your yticks for a log plot. As log(0) is minus infinity the distance between tick 0 and tick 0.01 will be much too large. You can choose another small but positive value for the smallest y, e.g. 0.0001, depending on your data

Answered in the comment above by JohanC.

edited May 19, 2020 at 16:47

BigBen

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answered May 19, 2020 at 16:30

Thomas Sloan

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