Compute Partial Transcriptome Evolutionary Index (TEI) Strata Values

This function computes the partial transcriptome evolutionary index (TEI) values combined for each strata.

In detail, each gene gets a TEI contribution profile.

$$TEI_is = f_is * ps_i$$

where TEI_is is the partial TEI value of gene i, \(f_is = e_is / \sum e_is\) and \(ps_i\) is the phylostratum of gene i.

\(TEI_is\) values are combined per \(ps\).

pStrataTEI(
  ExpressionSet,
  Phylostratum = NULL,
  by = NULL,
  groups = NULL,
  split = 1e+05,
  showprogress = TRUE,
  threads = 1
)

Arguments

ExpressionSet

expression object with rownames as GeneID (dgCMatrix) or standard PhyloExpressionSet object.

Phylostratum

a named vector representing phylostratum per GeneID with names as GeneID (not used if Expression is PhyloExpressionSet).

by

specify min/max transformation by row (stages, cells, celltypes) or by column (phylostratum)

groups

specify stages or cells to be grouped into celltypes by a named list

split

specify number of columns to split

showprogress

boolean if progressbar should be shown

threads

specify number of threads

Value

a numeric matrix storing the summed partial TEI values for each strata.

Details

The partial TEI values combined per strata give an overall impression of the contribution of each strata to the global TEI pattern.

References

Domazet-Loso T. and Tautz D. (2010). A phylogenetically based transcriptome age index mirrors ontogenetic divergence patterns. Nature (468): 815-818.

Quint M et al. (2012). A transcriptomic hourglass in plant embryogenesis. Nature (490): 98-101.

Drost HG et al. (2015) Mol Biol Evol. 32 (5): 1221-1231 doi:10.1093/molbev/msv012

Author

Kristian K Ullrich

Examples

## get Seurat object
celegans<-readRDS(file=system.file("extdata",
    "celegans.embryo.SeuratData.rds", package="scTEI")
)

## load Caenorhabditis elegans gene age estimation
celegans_ps<-readr::read_tsv(
   file=system.file("extdata",
   "Sun2021_Orthomap.tsv", package="scTEI")
)
#> Rows: 20040 Columns: 2
#> ── Column specification ────────────────────────────────────────────────────────
#> Delimiter: "\t"
#> chr (1): GeneID
#> dbl (1): Phylostratum
#> 
#> ℹ Use `spec()` to retrieve the full column specification for this data.
#> ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.

## define Phylostratum
ps_vec<-setNames(
    as.numeric(celegans_ps$Phylostratum),
    celegans_ps$GeneID
)

## get partial TEI strata values
Seurat::Idents(celegans)<-"embryo.time.bin"
pSt<-pStrataTEI(
    ExpressionSet=Seurat::GetAssayData(celegans, assay="RNA", layer="counts"),
    Phylostratum=ps_vec
)

## get partial TEI strata values per cell group
Seurat::Idents(celegans)<-"embryo.time.bin"
cell_groups<-Ident2cellList(Seurat::Idents(celegans))
pSt<-pStrataTEI(
   ExpressionSet=Seurat::GetAssayData(celegans, assay="RNA", layer="counts"),
   Phylostratum=ps_vec,
   groups=cell_groups
)
p1<-ComplexHeatmap::Heatmap(
    pSt,
    name="pSt",
    column_title="partial TEI values - cell groups",
    row_title="More Recent <<< More Ancient",
    cluster_rows=FALSE,
    cluster_columns=FALSE,
    col=viridis::viridis(3)
)
p1


## get relative expression over stages per cell group
Seurat::Idents(celegans)<-"embryo.time.bin"
cell_groups<-Ident2cellList(Seurat::Idents(celegans))
pSt<-pStrataTEI(
   ExpressionSet=Seurat::GetAssayData(celegans, assay="RNA", layer="counts"),
   Phylostratum=ps_vec,
   groups=cell_groups,
   by="row"
)
p2<-ComplexHeatmap::Heatmap(
    pSt,
    name="pSt",
    column_title="partial TEI values - cell groups - by row",
    row_title="More Recent <<< More Ancient",
    cluster_rows=FALSE,
    cluster_columns=FALSE,
    col=viridis::viridis(3)
)
p2


## get relative expression over phylostrata per cell group
Seurat::Idents(celegans)<-"embryo.time.bin"
cell_groups<-Ident2cellList(Seurat::Idents(celegans))
pSt<-pStrataTEI(
   ExpressionSet=Seurat::GetAssayData(celegans, assay="RNA", layer="counts"),
   Phylostratum=ps_vec,
   groups=cell_groups,
   by="column"
)
p3<-ComplexHeatmap::Heatmap(
    pSt,
    name="pSt",
    column_title="partial TEI values - cell groups - by col",
    row_title="More Recent <<< More Ancient",
    cluster_rows=FALSE,
    cluster_columns=FALSE,
    col=viridis::viridis(3)
)
p3