## ----setup,echo=FALSE------------------------------------------------------ suppressPackageStartupMessages({ library(knitr) library(ontoProc) go = getGeneOnto() cl = getCellOnto() pr = getPROnto() library(ontologyPlot) library(BiocStyle) }) ## ----lksco----------------------------------------------------------------- kable(packDesc2019) ## ----lklk------------------------------------------------------------------ kable(stab <- seur3kTab()) ## ----lklklk---------------------------------------------------------------- library(ontoProc) cl = getCellOnto() onto_plot2(cl, stab$tag) ## ----lkfa------------------------------------------------------------------ kable(CLfeats(cl, "CL:0002531")) ## ----lksy------------------------------------------------------------------ kable(sdf <- as.data.frame(sym2CellOnto("ITGAM", cl, pr))) table(sdf$cond) kable(as.data.frame(sym2CellOnto("FOXP3", cl, pr))) ## ----lksig----------------------------------------------------------------- sigels = c("CL:X01"="GRIK3", "CL:X02"="NTNG1", "CL:X03"="BAGE2", "CL:X04"="MC4R", "CL:X05"="PAX6", "CL:X06"="TSPAN12", "CL:X07"="hSHISA8", "CL:X08"="SNCG", "CL:X09"="ARHGEF28", "CL:X10"="EGF") ## ----lkdfff---------------------------------------------------------------- cs = cyclicSigset(sigels) dim(cs) cs[c(1:5,9:13),] table(cs$cond) ## ----lklk1----------------------------------------------------------------- makeIntnProlog = function(id, ...) { # make type-specific prologs as key-value pairs c( sprintf("id: %s", id), sprintf("name: %s-expressing cortical layer 1 interneuron, human", ...), sprintf("def: '%s-expressing cortical layer 1 interneuron, human described via RNA-seq observations' [PMID 29322913]", ...), "is_a: CL:0000099 ! interneuron", "intersection_of: CL:0000099 ! interneuron") } ## ----doterm---------------------------------------------------------------- pmap = c("hasExp"="has_expression_of", lacksExp="lacks_expression_of") head(unlist(tms <- ldfToTerms(cs, pmap, sigels, makeIntnProlog)), 20)