Created
March 4, 2020 14:26
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Running OHeLa500 Benchmark
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# 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) |
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