possible bug in plot_fst_gwss?

[EricRLucas]

Apologies if I'm wrong about this.

A colleague is running plot_fst_gwss with min_clip = -1, but is finding that the y axis range of the plot is always 0 to 1.

Looking at the source code, it looks to me like this is driven by lines 238 and 255 in anoph/fst.py. This is the definition for plot_fst_gwss_track, where the value y_range is set to (0,1) and the value fig.yaxis.ticker is set to [0, 1].

I think the y_range should be set appropriately for the range of Fst that come out in the calculations. Otherwise, changing min_clip doesn't serve, because the values don't get displayed anyway.

Perhaps the minimum value of the y axis could be np.min([0, np.min(fst)]. Max value can be kept at 1 for consistency if desired.

Thanks

Eric

[alimanfoo]

Thanks @EricRLucas, that sounds very reasonable.

[alimanfoo]

Suggest to use the min_clip parameter value as the lower bound on the Y axis limits.

[EricRLucas]

Thanks Alistair