How to use Cyclone to predict cell cycle from single cell Multiomic data (scRNA part)

Question

[halimaakhter014]

This is the code I am using to predict cell cycle phases. But I keep getting NA from the final output. I am using Gene Expression part from the single cell multiomic data that means it contains scRNA and scATAC both.

library(Seurat)
library(Signac)
library(EnsDb.Hsapiens.v86)
library(dplyr)
library(ggplot2)
library(tidyverse)
library(scran)

hs.pairs <<- readRDS(system.file("exdata", "human_cycle_markers.rds", package="scran"))

myFunction <- function(colnam){
  first_column <- hs.pairs[[1]][colnam]
  print(first_column)
  unique_f_value <- unique(first_column)
  cv_unique_f_value <- unlist(unique_f_value)

  print(cv_unique_f_value)

  print(length(cv_unique_f_value))
  print(unique_f_value)



  return(cv_unique_f_value)
}



u1 <- myFunction ("first")
u2 <- myFunction ("second")


srt1 <- Read10X_h5("D:/Halima's Data/Thesis/single_cell_data/filtered_feature_bc_matrix.h5")
# extract RNA and ATAC data
rna_counts_srt1 <- srt1$`Gene Expression`

count_matrix <- as.matrix(rna_counts_srt1)


geneID_col_first <- ensembldb::select(EnsDb.Hsapiens.v86, keys= u1, keytype = "GENEID", columns = c("SYMBOL","GENEID"))

geneID_col_second <- ensembldb::select(EnsDb.Hsapiens.v86, keys= u2, keytype = "GENEID", columns = c("SYMBOL","GENEID"))

# Replace ensemble IDs with gene symbols in hs.pairs[[1]]$first
gene_symbols_first <- geneID_col_first$SYMBOL
hs.pairs[[1]]$first <- gene_symbols_first[match(hs.pairs[[1]]$first, geneID_col_first$GENEID)]

# Replace ensemble IDs with gene symbols in hs.pairs[[1]]$second
gene_symbols_second <- geneID_col_second$SYMBOL
hs.pairs[[1]]$second <- gene_symbols_second[match(hs.pairs[[1]]$second, geneID_col_second$GENEID)]

print(hs.pairs[[1]]$first)

print(hs.pairs[[1]]$second)

row_names <- rownames(count_matrix)
print(row_names)
assignments <- cyclone(count_matrix,pairs=hs.pairs)

print(assignments)

plot(assignments$score$G1, assignments$score$G2M,
     xlab="G1 score", ylab="G2/M score", pch=16)

when I print this:

print(assignments)

I get this :

       G1  S G2M
1   0.000 NA  NA
2   0.003 NA  NA
3   0.000 NA  NA
4   0.000 NA  NA
5   0.000 NA  NA
6   0.010 NA  NA
7   0.000 NA  NA
..
..

The plot function doesn't show anything. Somebody help me!

[Alexander]

Sorry cannot answer that question directly, but in general Cyclone is quite old package not really working well for cell cycle scRNA-seq data. I would recommend ”Tricycle”. See survey of different methods: https://arxiv.org/abs/2208.05229

[halimaakhter014]

Thank you for trying though!