Obtain the top signature genes and related information.
get.top.signature.dat(df.list, ntop = 5, expr.prop.cutoff = 0.1)a list that is obtained by the function find.signature.genes.
an optional positive integer, specify the how many top signature genes extracted, default as 5.
an optional postive real ranging from 0 to 1, specify cutoff of expression proportion of features, default as 0.1.
return a `data.frame` object with four columns: `distance`,`expr.prop`, `label` and `gene`.
Using this funciton, we obtain the top signature genes and organize them into a data.frame. The `row.names` are gene names. The colname `distance` means the distance between gene (i.e., VPREB3) and cells with the specific cell type (i.e., B cell), which is calculated based on the coembedding of genes and cells in the coembedding space. The distance is smaller, the association between gene and the cell type is stronger. The colname `expr.prop` represents the expression proportion of the gene (i.e., VPREB3) within the cell type (i.e., B cell). The colname `label` means the cell types and colname `gene` denotes the gene name. By the data.frame object, we know `VPREB3` is the one of the top signature gene of B cell.
None
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library(Seurat)
data(pbmc3k_subset)
pbmc3k_subset <- pdistance(pbmc3k_subset, reduction='ncfm')
#> Calculate co-embedding distance...
df_list_rna <- find.signature.genes(pbmc3k_subset)
#>
| | 0 % ~calculating
|++++++ | 11% ~00s
|++++++++++++ | 22% ~00s
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|++++++++++++++++++++++++++++ | 56% ~00s
|++++++++++++++++++++++++++++++++++ | 67% ~00s
|+++++++++++++++++++++++++++++++++++++++ | 78% ~00s
|+++++++++++++++++++++++++++++++++++++++++++++ | 89% ~00s
|++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=00s
dat.sig <- get.top.signature.dat(df_list_rna, ntop=5)
#>
| | 0 % ~calculating
|++++++ | 11% ~00s
|++++++++++++ | 22% ~00s
|+++++++++++++++++ | 33% ~00s
|+++++++++++++++++++++++ | 44% ~00s
|++++++++++++++++++++++++++++ | 56% ~00s
|++++++++++++++++++++++++++++++++++ | 67% ~00s
|+++++++++++++++++++++++++++++++++++++++ | 78% ~00s
|+++++++++++++++++++++++++++++++++++++++++++++ | 89% ~00s
|++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=00s
head(dat.sig)
#> distance expr.prop label gene
#> TCL1A 0.02557952 0.6220930 B TCL1A
#> CD79A 0.02854258 0.9360465 B CD79A
#> IRF8 0.03268292 0.3750000 B IRF8
#> IGLL5 0.03337475 0.2325581 B IGLL5
#> PPP1R14A 0.03610722 0.1250000 B PPP1R14A
#> FPR1 0.06510844 0.4270833 CD14+ Mono FPR1