Running OHeLa500 Benchmark

ohelahela.R

# Comparing different executions of the same isoquant projects
# install.packages("igraph")
library(LFQBench2)
library(stringr)
library(igraph)
library(purrr)

is.error <- function(x) inherits(x, "try-error")
dp = "/mnt/ms/symphony/HELA_BENCHMARK/2020_02_18/REPEAT_WITH_SETTINGS_OF_TeslaS/"
comps = list.files(dp)

peptides_names = Sys.glob(file.path(dp,'*.csv'))
names(peptides_names) = sapply(str_split(basename(peptides_names), '_OHe[Ll]a500_'), '[',1)

proteins_names = Sys.glob(file.path(dp,'*.xlsx'))
names(proteins_names) = sapply(str_split(basename(proteins_names), '_OHe[Ll]a500_'), '[',1)

peptides = lapply(peptides_names, function(x) try({read_wide_report(x)}))
proteins = lapply(proteins_names, function(x) try({read_wide_report(x, skip=1, sheet="TOP3 quantification")}))

any(sapply(peptides, is.error))
any(sapply(proteins, is.error))

comparator = function(x){
  A = x[[1]]
  B = x[[2]]
  if((nrow(A) == nrow(B))&(ncol(A) == ncol(B))){ return(all(A==B, na.rm=T)) }
  else{
    return(FALSE)
  }
}

compare_reportes = function(x, I_col_pattern, additional_cols=NULL){
  x_I_all = lapply(x, get_intensities, I_col_pattern=I_col_pattern)
  x_I = lapply(x_I_all, '[[',1)
  if(!is.null(additional_cols)){
    more_cols = lapply(x, function(y) y[,additional_cols, with=F])
    x_I = map2(x_I, more_cols, cbind)
  }
  x_designs = lapply(x_I_all, '[[', 2)
  design = x_designs[[1]]
  icols = as.character(design$I_col_name)
  x_ord_I = lapply(x_I,function(x){
                        setorderv(x, cols=icols)
                        x
                      })
  x_ord = lapply(peptides, function(x) x[order(sequence, modifier, type)])
  res = combn(x_ord_I, 2, simplify=T, FUN=comparator)
  n = combn(names(x), 2)
  names(res) = paste(n[1,], n[2,], sep=':')
  res
}

GP = compare_reportes(peptides, "intensity in .* (:cond:.)", c('sequence', 'modifier'))
all(GP)
GR = compare_reportes(proteins, 'OHe.* (:cond:.)', c('accession', 'entry'))
all(GR)

to_graph = function(r, directed=F, ...){
  df = str_split(names(r),':', simplify=T)[r,]
  graph_from_data_frame(df, directed=directed, ...)
}

gp = to_graph(GP)
plot(gp)

gr = to_graph(GR)
plot(gr)