Closed france-hub closed 1 year ago
To compute the ratio you want, yes, that looks right. Though I'd use base R for this (simpler than plotting, pulling out data, and using fancy tidy stuff)...
> # setup from package example data
> library(CATALYST)
> data(PBMC_fs, PBMC_panel, PBMC_md)
> sce <- prepData(PBMC_fs, PBMC_panel, PBMC_md)
> sce <- cluster(sce, verbose = FALSE)
>
> # specify clustering of interest
> k <- "meta10"
> kids <- cluster_ids(sce, k)
> # cell counts by sample-cluster
> ns <- table(sce$sample_id, kids)
> # get proportions
> fq <- prop.table(ns, 1)
> fq[seq(6), seq(4)]
kids
1 2 3 4
Ref1 0.253121453 0.177071510 0.007945516 0.047673099
Ref2 0.292237443 0.228310502 0.015981735 0.020547945
Ref3 0.180303030 0.198484848 0.019696970 0.113636364
Ref4 0.198945982 0.125164690 0.005270092 0.047430830
BCRXL1 0.229166667 0.035984848 0.013257576 0.049242424
BCRXL2 0.215037594 0.085714286 0.007518797 0.019548872
> # these sum to 1 across samples, i.e.,
> # relative cluster abudance across samples
> all(rowSums(fq) == 1)
[1] TRUE
> # ratio betwee clusters 3 & 8
> fq[, "3"]/fq[, "8"]
Ref1 Ref2 Ref3 Ref4 BCRXL1
0.02916667 0.07692308 0.19402985 0.03846154 0.03608247
BCRXL2 BCRXL3 BCRXL4
0.02272727 0.04819277 0.03053435
But whether this is a sound approach to test "whether the ratio between two subsets is significantly enriched in one or more of the conditions" I am not sure.
The typical approach here would be differential abundance (DA) analysis across all subpopulations that also accounts for composition effects. E.g., if another subpopulation (not considered in the ratio) drastically changes (in abundance), this might affect other subpopulations in their relative abundance. Now, if the two subpopulations you're considering or different samples are affected differently, their ratio might change, though it's a side-effect of the "bigger picture".
I admit this is a vague and not at all a statsy argument, but my intuition is that one wants to model the whole data to draw any conclusions vs. pulling out a comparison of interest only. Perhaps @lmweber, author of the diffcyt
package that implements DA analysis in this framework, has some better thoughts?
Ok got it! Thanks for your answer. I’ll wait then for Weber’s opinion too.
Hello Helena,
Feel free to close this if you need to, you gave me a really satisfactory answer. If needed I'll open a diffcyt
issue.
Thanks! Francesco
Hello Helena, I have been asked to understand whether the ratio between two subsets is significantly enriched in one or more of the conditions in my dataset.
I tried to get the ratio using Catalyst, but I do not know if what I am doing is correct:
Does this sound right?
Thanks! Francesco