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[Update]: We have just released v1.9.0 with Logarithmic Axis. Please checkout gallery page for Logarithmic Scale.
In case you are using labelFormatter for implementing logarithmic axisY it will override valueFormatString. So, in this case inside labelFormatter function in the CanvasJS.formatNumber method you have to pass required format as second argument. Eg. in the example of logarithmic axisY by rewriting line 12 as below would remove the comma.
lable = CanvasJS.formatNumber(lable/1000, "####") +"k";