After browsing the code, it appears that neither GD::Chart nor GD::Graph supports log axes. Indeed, there is a request for just this in the GD::Graph bug list. GD::Chart does not seem to have been updated for about five years; I wonder if it's no longer being worked on.
One workaround would be to convert your (x,y) pairs to (x,log10(y)), but this won't look quite the same as would plotting a logarithmic axis, like you would get plotting on semi-log paper..
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