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edward130603 / BayesSpace

Bayesian model for clustering and enhancing the resolution of spatial gene expression experiments.
http://edward130603.github.io/BayesSpace
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Missing clusters when cluster at k = 28 #80

Open abspangler13 opened 2 years ago

abspangler13 commented 2 years ago

Hello,

I ran BayesSpace with k = 28 for ~113,000 spots. I've noticed that I only get 26 clusters because clusters 18 and 21 are missing. Is this to be expected? Is it possible, BayesSpace is merging small clusters?

> table(csv$cluster,useNA = "ifany")

    1     2     3     4     5     6     7     8     9    10    11    12    13 
 3100  4455  7686 10108  7161  3486  5752  3063  9308  6014  2473  2340  6212 
   14    15    16    17    19    20    22    23    24    25    26    27    28 
 9573  3480  5694  3417  2745  2498  1799  1609  3165  2487  2145   877  3280 
> nrow(csv)
[1] 113927

Thanks,

Abby cc @lcolladotor

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edward130603 commented 2 years ago

Hi Abby, yes I have seen this happen before in other data as well. In such cases, BayesSpace's model finds better partitions of the data using fewer clusters. The spatial smoothing BayesSpace applies penalizes neighboring spots with different cluster labels, so if you have two clusters (in your initialization) that are fairly similar, BayesSpace may combine them.

One way to get around this potentially is by reducing the value of the smoothing parameter gamma. Trying a different initialization may also help here since you have a pretty large dataset.

lcolladotor commented 2 years ago

Thank for the info Edward! Thanks for the confirmation that you've seen this before and for the info on gamma.

I think that we'll be ok with k_obs <= k_input. Abby, I think that you can close this issue.

Best, Leo