Mislabelled subtype numbers in PVDs about pysustain

[sea-shunned]

Hi Beatrice, thanks for raising this. Just to clarify, are you saying that the subtype labelled in the PVD, e.g. "Subtype 2", may represent individuals that are not labelled as 2 in ml_subtype? (Ignore 0 vs 1 indexing for the purposes of this)

[Bea-Taylor]

Hi Cameron, yes. For example, according to the PVD I have (n=55) in "Subtype 3", and (n=59) in "Subtype 4", however when I look at the output of ml_subtype I have (n=59) in "Subtype 3" and (n=55) in "Subtype 4".

[noxtoby]

Probably the fault of the plotting routines

[sea-shunned]

The PVD order is (usually) defined as:

pySuStaIn/pySuStaIn/AbstractSustain.py

Line 217 in a7d2e26

self._plot_subtype_order = np.argsort(ml_f_EM)[::-1]

whereas from a quick glance the ml_subtype order is defined as:

pySuStaIn/pySuStaIn/AbstractSustain.py

Lines 534 to 535 in a7d2e26

	temp_mean_f = np.mean(samples_f, axis=1)
	ix = np.argsort(temp_mean_f)[::-1]

Both refer to the subtype size, but the former is from the size in the final EM step for that N-subtype model (whatever pickle file you have loaded), whereas the latter comes from the proportion over the MCMC samples (if I am not mistaken).

These should usually be the same, but I guess for slight differences like this they diverge. A quick fix would be to calculate both the same way. Before doing this, it's good to check that there wasn't a deliberate reason that each method was used where it was. @LeonAksman do you know? If there's no strong reason, we can replace one with the other. Possibly best to use the MCMC version, but that's just my opinion, happy to hear others.

[ayoung11]

I think the problem is to do with the plotting routines. One possible issue is the one Cameron mentioned. But the other issue that keeps cropping up is that the number of subjects in the plotting routines is calculated using the model fraction multiplied by the number of subjects (see e.g. line 629 in ZscoreSustain.py). This gives a different output to assigning individuals to their maximum likelihood subtype because the fraction indicates the expected proportion of individuals rather than the actual proportion of individuals. So it's also possible that what appears as switching (n=59) to (n=55) may actually be a coincidence in this case due to the discrepancy in the way of calculating the number between the PVDs and ml_subtype. I would suggest the following:

(a) The PVDs should be altered to calculate the number based on ml_subtype (or for now just display the fraction)

(b) In the PVDs we use samples_f to order the subtypes, consistent with ml_subtype

I found another bug in the plotting too for the colours of the z-score model when the number of z-scores is greater than three so planning to work on both issues as soon as I can manage to get to them. If you were planning on making changes yourself Cameron we could discuss and coordinate - let me know via email.

[biondof]

Hi! I also encountered this problem in multiple ways. For example, the PVD indicates subtype1 n=494 and subtype2 n=296. However, the output table suggests completely different numbers, subtype1=726 and subtype2=64. In addition, the cross-validation occasionally flips the subtypes, such that the cross-validated PVD for subtype1 from looks like the PVD for subtype 2 from the non-cross-validated result (rather than being consistent with the labelling). Finally, as @ayoung11 mentions, the colour for z-score 4 is pink which makes it confusing to read as z-score 2 is also pink.

[sea-shunned]

Grappled with this a little bit recently so adding thoughts here. When attributing names to the subtypes, and plotting with e.g. stage zero individuals removed, one may want to change the order of the PVDs. Trying to change this can lead to unexpected situations where the link between ml_subtype == 1 and "Subtype 1" is broken, particularly as the order is probably already different to begin with. This then gets unintuitive, as using the subtype_order argument will not lead to expected results. For example, you may want to e.g. reverse the order entirely. For a 3 subtype model, you could then add subtype_order=[2,1,0] when calling the plot_positional_var method, but if the default subtype order (calculated as np.argsort(ml_f_EM)[::-1]) is not [0,1,2] then the result will not be the subtypes in reverse order. Thus the correspondance between ml_subtype and what is shown in the PVDs becomes unclear and confusing, and can no doubt lead to issues.

To address this, in addition to making the numbers more reflective as discussed above, there probably should be no reordering of subtypes by default, ensuring that the order shown in the PVD is always reflective of the numbers in ml_subtype. Custom reordering is then an option of course, but in that scenario the user will be fully aware that it is being done and what it therefore means.

Happy to hear thoughts on this so we can try and fix this issue.

[noxtoby]

Definitely agree that the default should be no reordering.

This doesn't solve the CV situation, where one subsample (/fold) could produce a different set of subtypes, making combination across folds...challenging at best. How to best handle this will depend on the goal of the CV experiment.

[Zeena-Shawa]

Just wanted to confirm that @sea-shunned's comment on the unclear correspondence between the default PVD order and subtype_order method is definetely true. For my analysis I have 11 subtypes and had to order as follows to get the same order as provided by ml_sequence_EM: subtype_order = [0,7,8,4,6,1,10,5,9,3,2], and this order does not correspond to just ordering what is seen on the PVD, nor to the indices of the re-ordering (not sure what it does correspond to).

Grappled with this a little bit recently so adding thoughts here. When attributing names to the subtypes, and plotting with e.g. stage zero individuals removed, one may want to change the order of the PVDs. Trying to change this can lead to unexpected situations where the link between ml_subtype == 1 and "Subtype 1" is broken, particularly as the order is probably already different to begin with. This then gets unintuitive, as using the subtype_order argument will not lead to expected results. For example, you may want to e.g. reverse the order entirely. For a 3 subtype model, you could then add subtype_order=[2,1,0] when calling the plot_positional_var method, but if the default subtype order (calculated as np.argsort(ml_f_EM)[::-1]) is not [0,1,2] then the result will not be the subtypes in reverse order. Thus the correspondance between ml_subtype and what is shown in the PVDs becomes unclear and confusing, and can no doubt lead to issues.

To address this, in addition to making the numbers more reflective as discussed above, there probably should be no reordering of subtypes by default, ensuring that the order shown in the PVD is always reflective of the numbers in ml_subtype. Custom reordering is then an option of course, but in that scenario the user will be fully aware that it is being done and what it therefore means.

Happy to hear thoughts on this so we can try and fix this issue.