naive polygon viewer, will indicate presence of transcripts for two genes in cells

view_seg_g2(x, xlim, ylim, gene1, gene2, show_tx = FALSE, ...)

Arguments

x: instance of XenSCE
xlim: numeric(2) ordered vector of max and min on x
ylim: numeric(2) ordered vector of max and min on y
gene1: character(1) gene to be checked, cell polygon will be filled if gene has non-zero count
gene2: character(1) gene to be checked, cell polygon will be filled if gene has non-zero count
show_tx: logical(1) display transcript locations if TRUE, defaults to FALSE.
...: passed to polygon()

Value

Primarily for plotting. A list is invisibly returned with elements polys, ncells and call.

Note

This is more RAM-sparing than clip_rect followed by view. Colors are pre-assigned for individual and joint occupancies in this draft of this visualizer.

Examples

luad = cache_xen_luad()
pa = cache_xen_luad()
luad = restoreZipXenSPEP(pa)
rownames(luad) = make.names(SummarizedExperiment:::rowData(luad)$Symbol, unique=TRUE)
out = view_seg_g2(luad, c(5800, 6300), c(1300, 1800), lwd=.5, gene1="CD4", gene2="EPCAM")
#> Parquet geometry data untouched by subsetting.  Affects SpatialExperiment content only
#> Parquet geometry data untouched by subsetting.  Affects SpatialExperiment content only
legend(5800,1370, fill=c("cyan", "purple", "pink"), legend=c("CD4", "EPCAM", "both"))

out$ncells
#> [1] 2074