## ----setup,echo=FALSE,results="hide"，message=FALSE---------------------------- library(knitr) library(ontoProc) cl = getOnto("cellOnto"， "2021") # for continuity——has_high_plasma_膜量:list # has_low_plasma_膜量:列表出现在2021年而不是2022年-似乎这些已经#移动到RO(关系本体)#> grep(“等离子”，nn，值=TRUE) # RO:0002104 RO:0015015 #“有质膜部分”“有高质膜量”# RO:0015016 #“有低质膜量”# go = getOnto(“goOnto”)pr = getOnto(“PROnto”)库(ontologyPlot)库(BiocStyle)库(singlecel实验)库(celldex) ## ----setup2，message=FALSE---------------------------------------------------- library(ontoProc) library(ontologyPlot) library(BiocStyle) # for package references cl = getOnto("cellOnto"， "2021") # for continuity——has_high_plasma_膜e_amount: list go = getOnto("goOnto"， "2021") #如果更新，一些断言将失败…公关= getOnto(“很快地”、“2021 ") ## ---- lksco -------------------------------------------------------------------- 数据(packDesc2022) kable (packDesc2022 [- c (1) 7 )]) ## ---- lklk --------------------------------------------------------------------- kable (< - seur3kTab刺 ()) ## ---- lklklk ------------------------------------------------------------------- 图书馆(ontoProc) cl = getOnto(“cellOnto”、“2021”)onto_plot2 (cl,刺标签)# #——lkfa美元 --------------------------------------------------------------------- suppressMessages ({kable (CLfeats (cl, cl: 0002531,公关=公关,去= )) }) ## ---- lksy --------------------------------------------------------------------- kable (sdf < as.data.frame (sym2CellOnto(“ITGAM”,cl,公关)))表(sdf电导率美元)kable (as.data.frame (sym2CellOnto(“具体”,cl,公关 ))) ## ---- lksig -------------------------------------------------------------------- sigels = c(“CL: X01”=“GRIK3”,“CL: X02”=“NTNG1”,“CL: X03”=“BAGE2”,“CL: X04”=“中的”、“CL: X05”=“PAX6”,“CL: X06”=“TSPAN12”,“CL: X07”=“hSHISA8”,“CL:(”=“SNCG”,“CL: X09”=“ARHGEF28”,“CL: X10”=“EGF ") ## ---- lkdfff ------------------------------------------------------------------- c = cyclicSigset (sigels)暗(cs) cs (c(1:5, 13))表(cs电导率美元)# #——lklk1 -------------------------------------------------------------------- makeIntnProlog =函数(id , ...) { # 使特定类型的prolog键-值对c (sprintf (id: % s, id), sprintf(“名字:%s表达皮层1层中间神经元，人类"，…)，sprintf("def: '%s表达皮层1层中间神经元，人类通过RNA-seq观测描述' [mmid 29322913]"，…)，"is_a: CL:0000099 !interneuron"， "intersection_of: CL:0000099 !中间神经原 ") } ## ---- doterm ------------------------------------------------------------------- pmap = c(“hasExp”=“has_expression_of”,lacksExp =“lacks_expression_of”)(unlist (tms <——ldfToTerms (cs, pmap sigels, makeIntnProlog)), 20) # #——lkmap -------------------------------------------------------------------- hpca_map = read.csv(执行(“extdata / hpca.csv”、包=“ontoProc”),字符串= FALSE)头(hpca_map) # #——多伦 -------------------------------------------------------------------- 名称(hpca_map) = c(“非正式”、“正式的”)#现在的# #,gethpca eval = TRUE ------------------------------------------------------- 库(SingleCellExperiment)库(celldex) hpca_sce = HumanPrimaryCellAtlasData () ## ---- dobind eval = TRUE -------------------------------------------------------- hpca_sce = bind_formal_tags (hpca_sce”标签。好”,hpca_map)长度(独特的(hpca_sce label.ont美元 )) ## ---- justna eval = TRUE -------------------------------------------------------- 长度(xx <——(is.na (hpca_sce label.ont美元)))如果(长度(xx) > 0)打印(colData (hpca_sce) [xx,])和(hpca_sce $标签。ont == "", na.rm=TRUE) # iPS and BM ## ----dosub, eval=TRUE--------------------------------------------------------- cell_onto = ontoProc::getOnto("cellOnto", "2021") hpca_mono = subset_descendants( hpca_sce, cell_onto, "^monocyte$" ) table(hpca_mono$label.fine) table(hpca_mono$label.ont) # not much diversity hpca_tcell = subset_descendants( hpca_sce, cell_onto, "^T cell$" ) table(hpca_tcell$label.fine) table(hpca_tcell$label.ont) # uu = unique(hpca_tcell$label.ont) onto_plot2(cell_onto, uu) ## ----lkefo-------------------------------------------------------------------- ef = getOnto("efoOnto") alla <- grep("sthma", ef$name, value=TRUE) aa <- grep("obso", alla, invert=TRUE, value=TRUE) onto_plot2(ef, names(aa)) ## ----lkhdo,eval=FALSE--------------------------------------------------------- # hdo_2022_09 = get_OBO( # "https://github.com/DiseaseOntology/HumanDiseaseOntology/raw/main/src/ontology/HumanDO.obo", # extract_tags = "everything" # )