Closed caravagn closed 1 year ago
Fixed myself.
I fixed that but still it does not work.
It works with the default template fit released with the package
y = Rcongas::congas_example
y %>% Rcongas:::filter_clusters(ncells = 10, abundance = .5)
since
! Filtering 1 cluster due to low cell counts or abudance
ℹ No posterior probabilities, using euclidean distance to merge clusters
── [ Rcongas ] My CONGAS model n = 504 cells with k = 70 segments, grouped in k = 1 clusters. ───────────────
● Cluster 1, n = 504 [100% of total cells].
ℹ Model scored with BIC = 272839
● Differential Expression analysis for 1 vs 2 with the DESeq2 method: 212 DE genes at level alpha 0.01, with
|lfc| > 0.25.
But it does not work with a fit object @riccardobergamin which used
x <- Rcongas:::best_cluster(
x,
model = "MixtureGaussian",
clusters = 2:3,
steps = 500,
lr = 0.05,
param_list = list(theta_shape=5,theta_rate=1),
method = "BIC",
MAP = TRUE,
posteriors = FALSE,
step_post = 100)
> x
── [ Rcongas ] My CONGAS model n = 460 cells with k = 52 segments, grouped in k = 2 clusters. ───────────────
● Cluster c1, n = 348 [75.65% of total cells].
● Cluster c2, n = 112 [24.35% of total cells].
ℹ Model scored with BIC = 28574492.27
> x %>% Rcongas:::filter_clusters(ncells = 10, abundance = .5)
! Filtering 1 cluster due to low cell counts or abudance
ℹ No posterior probabilities, using euclidean distance to merge clusters
! Filtering 1 cluster due to low cell counts or abudance
ℹ No posterior probabilities, using euclidean distance to merge clusters
── [ Rcongas ] My CONGAS model n = 460 cells with k = 52 segments, grouped in k = 2 clusters. ───────────────
● Cluster c1, n = 348 [75.65% of total cells].
● Cluster c2, n = 112 [24.35% of total cells].
ℹ Model scored with BIC = 28574492.27
Besides, we should recompute the BIC score for the model etc after we remove some clusters.
Note that the default fit crashes with
y %>% Rcongas:::filter_clusters(ncells = 150, remove = TRUE)
with
Error in cm$parameters$assignment_probs[i, ] :
incorrect number of dimensions
Is this a thing? @Militeee
In https://github.com/Militeee/rcongas/blob/master/R/filter_clusters.R (function
remove_small_clusters
)get_best_model
cannot be called asbm <- Rcongas::get_best_model(x)
since it is not exported in https://github.com/Militeee/rcongas/blob/master/NAMESPACE.
Maybe this should be exported no?