Error during MapCODEXtoCITE() about stvea HOT 5 CLOSED

Hi, thanks for using our package.

The errors from the first section of code are generic errors produced by the parallelized mclapply function. You'll need to run the same MapCODEXtoCITE function with num_cores=1 to get usable error messages. Also, since that function is parallelized over the chunks of data, it is only reasonable to use num_cores < num_chunks, though I checked that it shouldn't produce an error if you go over.

The errors from the second section imply your parameters in the earlier functions do not match your parameters in the call to ScoreAnchors(). What are all of the variables shown in that code set to? It might help if you include your full code for the step by step pipeline, including variable and parameter assignments.

A few other clarification questions:

1. What environment are you running STvEA in? Are you using our Docker image? If not, what version of R are you using?
2. What are the dimensions of your CITE-seq and CODEX protein matrices, and how many proteins do they have in common? Please confirm that you have set row and column names for both matrices, and that stvea_object@codex_protein and stvea_object@cite_protein have the correct rows and columns (accounting for filtering).

from stvea.

Thanks for your reply. But I could resolve the issue. The problem was in sectioning/subsetting the codex data. There were very few cells upon subsetting. I changed the parameters to include more cells.

Although there is another issue I am facing in plotting the Cite seq data.

ggplot(stvea_object@cite_emb, aes_string(x = colnames(stvea_object@cite_emb)[1],  y = colnames(stvea_object@cite_emb)[2], color = factor(1:length(color)))) + geom_point(size = pt_size) + labs(title = paste(print_type,  "expression"), subtitle = subtitle) + scale_color_manual(values = alpha(color,  1), guide = FALSE) + theme_void()
Error: Aesthetics must be either length 1 or the same as the data (1310): colour
Run `rlang::last_error()` to see where the error occurred.

I tried removing color = factor(1:length(color)) and plot it. It gives me the plot but without colors. Example plots appear fine. Any clue what is happening?

Also, another error:

cite_cluster_adj <- AdjScoreClustersCITE(stvea_object, k=3, num_cores=8)
Error in cluster_matrix %*% t(transfer_matrix) : 
  Cholmod error 'X and/or Y have wrong dimensions' at file ../MatrixOps/cholmod_sdmult.c, line 88

Any insight is appreciated.

from stvea.

That makes sense. Sorry for the delay getting back to this.

I am assuming you are calling PlotExprCITE? The ggplot call probably doesn't work on its own outside of that function, since the color variable is not defined. The most likely reason you would be getting that error inside the PlotExprCITE function is if the mRNA or protein expression matrices do not have the same number of cells as the UMAP embedding matrix. Can you check the dimensions of stvea_object@cite_emb, stvea_object@cite_mRNA_norm, and stvea_object@cite_protein?

Your second error is also a dimensions issue - stvea_object@transfer_matrix should have the same number of columns as stvea_object@cite_clusters.

from stvea.

Thanks for pointing out. The dimensions of my latent space data and mRNA data were different. Getting latent space data for same no.of cells as mRNA solved the issue.

Another error I am facing is in GetUmapCODEX() call:

>stvea_object <- GetUmapCODEX(stvea_object, metric = 'pearson', n_neighbors=30, min_dist=0.1, negative_sample_rate = 50)
Error in if (abs(val - target) < tolerance) { : 
  missing value where TRUE/FALSE needed

>traceback()
5: smooth.knn.dist(knn$distance, nk, local.connectivity = connectivity, 
       bandwidth = bandwidth)
4: naive.fuzzy.simplicial.set(knn, config)
3: implementations[[method]](d, config)
2: umap::umap(stvea_object@codex_clean, ...)
1: GetUmapCODEX(stvea_object, metric = "pearson", n_neighbors = 30, 
       min_dist = 0.1, negative_sample_rate = 50)

Any suggestions would be appreciated.

from stvea.

Solved the above mentioned error.
It was caused due to the wrong codex_size information being loaded. It seems the codex_size variable is defined as we load the STvEA library. And the default variable is used in case we are not defining the codex_size variable by reading the size file. Probably a potential bug to be resolved in future updates.

from stvea.