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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.

axisY: {
      logarithmic: true,
      minimum: 0.00009,
      maximum: 10000,
      includeZero: true,
      interval: 1

Also, check out this updated JSFiddle for complete working code.

Setting minimum value for axisY

Manoj Mohan
Team CanvasJS