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@joshuasosa,
Sorry, controlling the first label to display on the axes is not available as of now. However to display axis label for 0.0001, you can set the minimum value of y-axis to 0.00009 in this case.
0.00009
axisY: { logarithmic: true, minimum: 0.00009, maximum: 10000, includeZero: true, interval: 1 }
Also, check out this updated JSFiddle for complete working code.
—- Manoj Mohan Team CanvasJS