pogos.R
In pogos: PharmacOGenomics Ontology Support

## ----setup,echo=FALSE---------------------------------------------------------
suppressMessages({
suppressPackageStartupMessages({
library(pogos)
library(S4Vectors)
library(DT)
library(ggplot2)
})
})

## ----lkcc---------------------------------------------------------------------
iric = iriCCLE()
iric 

## ----lkdrp--------------------------------------------------------------------
drp = DRProfSet()
drp

## ----lkpl090, fig.height=2.5--------------------------------------------------
plot(iric)

## ----lklll,fig.height=3.5-----------------------------------------------------
plot(drp)

## ----lkk, echo=FALSE----------------------------------------------------------
data(cell_lines_v1)
datatable(as.data.frame(cell_lines_v1), options=list(lengthMenu=c(3,5,10,50,100)))

## ----lkccc, echo=FALSE--------------------------------------------------------
data(compounds_v1)
datatable(as.data.frame(compounds_v1), 
   options=list(lengthMenu=c(3,5,10,50,100)))

## ----lkccc2, echo=FALSE-------------------------------------------------------
data(datasets_v1)
datatable(as.data.frame(datasets_v1))

## ----doch,fig=TRUE------------------------------------------------------------
library(ontoProc)
cc = getChebiOnto()
library(ontologyPlot)
onto_plot(cc, 
  c("CHEBI:134109", "CHEBI:61115", "CHEBI:75603", "CHEBI:37699", 
       "CHEBI:68481", "CHEBI:71178"), fontsize=24, shape="rect")

## ----lkmo, fig=TRUE-----------------------------------------------------------
onto_plot(cc, c("CHEBI:134109", "CHEBI:61115", "CHEBI:75603", "CHEBI:37699", 
   "CHEBI:68481", "CHEBI:71178", "CHEBI:52172", "CHEBI:64310", 
   "CHEBI:63632", "CHEBI:45863"), fontsize=28, shape="rect")

## ----ana,fig=TRUE-------------------------------------------------------------
clo = getCellLineOnto()
smoc = c("CLO:0000517", "CLO:0000560", "CLO:0000563", "CLO:0001072", 
"CLO:0001088", "CLO:0001138", "CLO:0007606")
onto_plot(clo, smoc)

## ----lkoo---------------------------------------------------------------------
library(ontoProc)
clo = getCellLineOnto()
minds = which(clo$name %in% c("143B cell", "1321N1 cell", "184B5 cell"))
tags = clo$id[minds]
clo$name[ unlist(clo$parent[tags]) ]

## ----lkefo, fig=TRUE----------------------------------------------------------
ee = getEFOOnto()
onto_plot(ee, c("UBERON:0000474", "UBERON:0000079", 
  "UBERON:0000990", "UBERON:0000995", "UBERON:0003982", 
  "UBERON:0000310", "UBERON:0002107", "UBERON:0001264", 
  "UBERON:0002113", "UBERON:0001007", "UBERON:0002530", 
  "UBERON:6007435", "UBERON:0004122", "UBERON:0001008"))

## ----lkcom--------------------------------------------------------------------
chl = getChebiOnto()
allch = chl$name
mm = allch[match(tolower(compounds_v1[,2]), tolower(allch), nomatch=0)]
round(length(mm)/nrow(compounds_v1),2) # not high
datatable(data.frame(id=names(mm), comp=as.character(mm)))

## ----srchsym, eval=FALSE------------------------------------------------------
#  notin = setdiff(compounds_v1$name, mm)
#  library(parallel)
#  options(mc.cores=2)
#  allch = tolower(allch)
#  notin = tolower(notin)
#  lk50 = mclapply(notin[1:50], function(x) { cat(x);
#         order(adist(x, allch))[1:5]})
#  names(lk50) = notin[1:50]
#  aa = do.call(cbind, lk50[1:50])
#  ttt = t(apply(aa,2,function(x) allch[x])[1:3,])

## ----lkcomb,cache=TRUE--------------------------------------------------------
library(rjson)
library(httr)
xx = GET("https://pharmacodb.pmgenomics.ca/api/v1/intersections/2/895/1?indent=true")
ans = fromJSON(readBin(xx$content, what="character"))
doses1 = sapply(ans[[1]]$dose_responses, function(x) x[[1]])
resp1 =  sapply(ans[[1]]$dose_responses, function(x) x[[2]])

## ----lkbar, fig=TRUE----------------------------------------------------------
library(ggplot2)
plot(DRTraceSet(dataset="CCLE"))