Check correspondence between "blindness" and "sensory_impairment" phenotypes

[bschilder]

@NathanSkene just discussed checking whether phenotypes that cause blindness also cause sensory impairments. There should be a strong correspondence between the two since blindness is technically a subset of sensory impairments.

@KittyMurphy would you mind looking into this?

[bschilder]

res_coded <- HPOExplorer::gpt_annot_codify()
cor.test(res_coded$annot_weighted$sensory_impairments, res_coded$annot_weighted$blindness)

    Pearson's product-moment correlation

data:  res_coded$annot_weighted$sensory_impairments and res_coded$annot_weighted$blindness
t = 104.79, df = 17479, p-value < 2.2e-16
alternative hypothesis: true correlation is not equal to 0
95 percent confidence interval:
 0.6119749 0.6301851
sample estimates:
      cor 
0.6211639 

Sensory impairments and blindness metrics are 62% correlated, which is a pretty decent correspondence. I'll add a note about this to the end of the results.

To take this further, may be helpful to have a (supp) fig showing the correlation between all severity metrics:

rc <- Hmisc::rcorr(as.matrix(res_coded$annot_weighted[,-c("hpo_id","hpo_name")]))
corrplot::corrplot(rc$r)

[bschilder]

Now under a short section in the Results and Methods called: Correlations between severity metrics