R/define_plan.R
In brandonsie/phipmake: PhIP-seq Data Analysis Pipeline
Defines functions
define_plan
Documented in
define_plan
#' Initialize and return drake_plan object. New for github drake 7.0+.
#'
#' @param params_path Path to project parameters file that can be created using the write_drake_params function.
#' @param runCounts Logical controlling whether or not to define counts targets.
#' @param runPairwise Logical controlling whether or not to define pairwise targets.
#' @param runFoldChange Logical controlling whether or not to define EdgeR fold change targets.
#' @param runEnrichment Logical controlling whether or not to define enrichment targets.
#' @param runPolyclonal Logical controlling whether or not to define enrichment targets.
#' @param runAVARDA Logical controlling whether or not to define AVARDA targets.
#' @param runEpitopefindr Logical controlling whether or not to run epitopefindr analysis on hits.
#' @param runEpitopefindr_nolatex Logical controlling whether or not to run epitopefindr analysis on hits without latex (replaces epitopefindr_latex).
#' @param e_thresh E value threshold for epitopefindr pairwise peptide sequence alignments. default 0.1.
#'
#' @export
#'
define_plan <- function(
params_path = "drake_params.tsv",
runCounts = TRUE,
runPairwise = FALSE,
runFoldChange = TRUE,
runEnrichment = TRUE,
runHits = TRUE,
runPolyclonal = TRUE,
runAVARDA = FALSE,
runEpitopefindr = FALSE,
runEpitopefindr_nolatex = FALSE,
e_thresh = 0.01
# epitopefindr_latex = FALSE
){
options(stringsAsFactors = FALSE)
# ============================================================================
# Settings
if(!file.exists(params_path)){
stop(paste("Params file missing.",
"If you haven't yet made a parameters file for this run,",
"try write_drake_params().",
"Curently looking for a parameters file named",
params_path, "in directory:", getwd()))
}
# Load parameters from drake_params.tsv
params <- data.table::fread(file_in(params_path))
# use_params <- c("screen_name", "counts_filename", "enrichment_filename",
# "enrichment_type", "enrichment_threshold", "metadata_path",
# "output_extension")
# for(i in 1:use_params){assign(i, getparam(params, i))}
screen_name <- getparam(params, "screen_name")
counts_filename <- getparam(params, "counts_filename")
counts_type <- getparam(params, "counts_type")
foldchange_filename <- getparam(params, "foldchange_filename")
foldchange_type <- getparam(params, "foldchange_type")
enrichment_filename <- getparam(params, "enrichment_filename")
enrichment_type <- getparam(params, "enrichment_type")
# enrichment_threshold <- getparam(params, "enrichment_threshold") %>% as.numeric
hits_filename <- getparam(params, "hits_filename")
metadata_path <- getparam(params, "metadata_path")
output_extension <- getparam(params, "output_extension")
output_separator <- getparam(params, "output_separator")
sublibrary_parallel <- as.logical(getparam(params, "sublibrary_parallel"))
# counts_libs <- getparam(params, "counts_libs")
# enrichment_libs <- getparam(params, "enrichment_libs")
# Establish sublibrary names
if(file.exists(counts_filename)){
temp.counts <- data.table::fread(counts_filename)
c.libs <- u_pep_id_to_libnames(temp.counts[,1])
c.lib.base <- c.libs[[2]]
c.libnames <- c.libs[[4]]
sn.lib.c <- paste0("_", c.libnames)
sn.libdir.c <- paste0(c.libnames, "/")
for(i in sn.libdir.c){if(!dir.exists(i)) dir.create(i)}
} else{
sn.lib.c <- sn.libdir.c <- "NA"
if(runCounts) {
warning(paste("Counts file is missing.",
"Are you in the right working directory?",
"Currently looking for a counts file named",
counts_filename, "in directory:", getwd()))
}
}
if(file.exists(enrichment_filename)){
temp.enrich <- data.table::fread(enrichment_filename)
e.libs <- u_pep_id_to_libnames(temp.enrich[,1])
e.lib.base <- e.libs[[2]]
e.libnames <- e.libs[[4]]
sn.lib.e <- paste0("_", e.libnames)
sn.libdir.e <- paste0(e.libnames, "/")
# Sublibrary directories create
for(i in sn.libdir.e){if(!dir.exists(i)) dir.create(i)
}
} else{
sn.lib.e <- sn.libdir.e <- "NA"
if(runEnrichment | runPolyclonal | runAVARDA){
warning(paste("Enrichment file is missing.",
"Are you in the right working directory?",
"Currently looking for an enrichment file named",
enrichment_filename, "in directory:", getwd()))
}
}
# ============================================================================
# Establish output file names
# ============================================================================
sn.ext <- paste0(".", output_extension)
sn.annot <- paste0("_annotated")
sn.a.ext <- paste0(sn.annot, sn.ext)
# Enrichment
sn.enrichment <- paste0(screen_name, "_", enrichment_type)
names.enrichment.pan <- paste0(sn.enrichment, sn.ext)
names.enrichment.pan.annot <- paste0(sn.enrichment, sn.a.ext)
sn.enrichment.sub <- paste0(sn.libdir.e, screen_name, sn.lib.e, "_", enrichment_type)
names.enrichment.sub <- paste0(sn.enrichment.sub, sn.ext)
names.enrichment.sub.annot <- paste0(sn.enrichment.sub, sn.a.ext)
# Promax
sn.enrichment.promax <- paste0(sn.enrichment, "_promax")
names.enrichment.promax.pan <- paste0(sn.enrichment.promax, sn.ext)
names.enrichment.promax.pan.annot <- paste0(sn.enrichment.promax, sn.a.ext)
sn.enrichment.promax.sub <- paste0(sn.libdir.e, screen_name, sn.lib.e, "_", enrichment_type, "_promax")
names.enrichment.promax.sub <- paste0(sn.enrichment.promax.sub, sn.ext)
names.enrichment.promax.sub.annot <- paste0(sn.enrichment.promax.sub, sn.a.ext)
# Hits
sn.hits <- paste0(screen_name, "_Hits")
names.hits.pan <- paste0(sn.hits, sn.ext)
names.hits.pan.annot <- paste0(sn.hits, sn.a.ext)
sn.hits.sub <- paste0(sn.libdir.e, screen_name, sn.lib.e, "_Hits")
names.hits.sub <- paste0(sn.hits.sub, sn.ext)
names.hits.sub.annot <- paste0(sn.hits.sub, sn.a.ext)
sn.hits.prosum <- paste0(sn.hits,"_prosum")
names.hits.pan.prosum <- paste0(sn.hits.prosum, sn.ext)
names.hits.pan.prosum.annot <- paste0(sn.hits.prosum, sn.a.ext)
sn.hits.prosum.sub <- paste0(sn.libdir.e, screen_name, sn.lib.e, "_Hits_prosum")
names.hits.sub.prosum <- paste0(sn.hits.prosum.sub, sn.ext)
names.hits.sub.prosum.annot <- paste0(sn.hits.prosum.sub, sn.a.ext)
sn.hits.foldchange.sub <- paste0(sn.hits.sub, "_foldchange")
names.hits.foldchange.sub <- paste0(sn.hits.foldchange.sub, sn.ext)
names.hits.foldchange.sub.annot <- paste0(sn.hits.foldchange.sub, sn.a.ext)
sn.hits.foldchange <- paste0(sn.hits, "_foldchange")
names.hits.foldchange.pan <- paste0(sn.hits.foldchange, sn.ext)
names.hits.foldchange.pan.annot <- paste0(sn.hits.foldchange, sn.a.ext)
sn.hits.foldchange.promax <- paste0(sn.hits.foldchange, "_promax")
names.hits.foldchange.pan.promax <- paste0(sn.hits.foldchange.promax, sn.ext)
names.hits.foldchange.pan.promax.annot <- paste0(sn.hits.foldchange.promax, sn.a.ext)
sn.hits.foldchange.promax.sub <- paste0(sn.hits.foldchange.sub, "_promax")
names.hits.foldchange.sub.promax <- paste0(sn.hits.foldchange.promax.sub, sn.ext)
names.hits.foldchange.sub.promax.annot <- paste0(sn.hits.foldchange.promax.sub, sn.a.ext)
sn.hits.enrichment.sub <- paste0(sn.hits.sub, "_enrichment")
names.hits.enrichment.sub <- paste0(sn.hits.enrichment.sub, sn.ext)
names.hits.enrichment.sub.annot <- paste0(sn.hits.enrichment.sub, sn.a.ext)
sn.hits.enrichment <- paste0(sn.hits, "_enrichment")
names.hits.enrichment.pan <- paste0(sn.hits.enrichment, sn.ext)
names.hits.enrichment.pan.annot <- paste0(sn.hits.enrichment, sn.a.ext)
sn.hits.enrichment.promax <- paste0(sn.hits.enrichment, "_promax")
names.hits.enrichment.pan.promax <- paste0(sn.hits.enrichment.promax, sn.ext)
names.hits.enrichment.pan.promax.annot <- paste0(sn.hits.enrichment.promax, sn.a.ext)
sn.hits.enrichment.promax.sub <- paste0(sn.hits.enrichment.sub, "_promax")
names.hits.enrichment.sub.promax <- paste0(sn.hits.enrichment.promax.sub, sn.ext)
names.hits.enrichment.sub.promax.annot <- paste0(sn.hits.enrichment.promax.sub, sn.a.ext)
sn.hits.counts.sub <- paste0(sn.hits.sub, "_counts")
names.hits.counts.sub <- paste0(sn.hits.counts.sub, sn.ext)
names.hits.counts.sub.annot <- paste0(sn.hits.counts.sub, sn.a.ext)
sn.hits.counts <- paste0(sn.hits, "_counts")
names.hits.counts.pan <- paste0(sn.hits.counts, sn.ext)
names.hits.counts.pan.annot <- paste0(sn.hits.counts, sn.a.ext)
# Polyclonal
sn.polycl <- paste0(screen_name, "_Polyclonal")
names.polycl.pan <- paste0(sn.polycl, sn.ext)
names.polycl.pan.annot <- paste0(sn.polycl, sn.a.ext)
sn.polycl.sub <- paste0(sn.libdir.e, screen_name, sn.lib.e, "_Polyclonal")
names.polycl.sub <- paste0(sn.polycl.sub, sn.ext)
names.polycl.sub.annot <- paste0(sn.polycl.sub, sn.a.ext)
# Counts
sn.counts <- paste0(screen_name, "_", counts_type)
names.counts.pan <- paste0(sn.counts, sn.ext)
names.counts.pan.annot <- paste0(sn.counts, sn.a.ext)
sn.counts.sub <- paste0(sn.libdir.c, screen_name, sn.lib.c, "_", counts_type)
names.counts.sub <- paste0(sn.counts.sub, sn.ext)
names.counts.sub.annot <- paste0(sn.counts.sub, sn.a.ext)
sn.counts.prosum <- paste0(sn.counts, "_prosum")
names.counts.prosum.pan <- paste0(sn.counts.prosum, sn.ext)
names.counts.prosum.pan.annot <- paste0(sn.counts.prosum, sn.a.ext)
sn.counts.prosum.sub <- paste0(sn.libdir.c, screen_name, sn.lib.c, "_", counts_type, "_prosum")
names.counts.prosum.sub <- paste0(sn.counts.prosum.sub, sn.ext)
names.counts.prosum.sub.annot <- paste0(sn.counts.prosum.sub, sn.a.ext)
# AVARDA
names.enrichment.avarda <- paste0(sn.enrichment.sub,
"_avardanames", sn.ext)
names.hits.avarda <- paste0(sn.hits.sub,
"_avardanames", sn.ext)
# Fold Change
sn.foldchange <- paste0(screen_name, "_", foldchange_type)
names.foldchange.pan <- paste0(sn.foldchange, sn.ext)
names.foldchange.pan.annot <- paste0(sn.foldchange, sn.a.ext)
sn.foldchange.sub <- paste0(sn.libdir.e, screen_name, sn.lib.e, "_", foldchange_type)
names.foldchange.sub <- paste0(sn.foldchange.sub, sn.ext)
names.foldchange.sub.annot <- paste0(sn.foldchange.sub, sn.a.ext)
# ============================================================================
# Plans
# --------------------------------------------------------------------------
# Parameters
# --------------------------------------------------------------------------
params_plan <- drake::drake_plan(
# Load parameters in plan environment
params = data.table::fread(file_in("drake_params.tsv")),
screen_name = getparam(params, "screen_name"),
counts_filename = getparam(params, "counts_filename"),
counts_type = getparam(params, "counts_type"),
enrichment_filename = getparam(params, "enrichment_filename"),
enrichment_type = getparam(params, "enrichment_type"),
# enrichment_threshold = getparam(params, "enrichment_threshold") %>% as.numeric,
hits_filename = getparam(params, "hits_filename"),
metadata_path = getparam(params, "metadata_path"),
output_extension = getparam(params, "output_extension"),
output_separator = getparam(params, "output_separator"),
sublibrary_parallel = as.logical(getparam(params, "sublibrary_parallel"))
)
# --------------------------------------------------------------------------
# Enrichment
if(runEnrichment) {
enrichment_plan <- drake::drake_plan(
enrichment = target(
data.table::fread(file_in(!!enrichment_filename))
), #10
write_enrichment = target(
write_data(enrichment, file_out(!!names.enrichment.pan))
),
enrichment_sub = target(
split_data(enrichment)
),
write_enrichment_sub = target(
write_data(enrichment_sub, file_out(!!names.enrichment.sub))
),
enrichment_annotations = target(
read_annot_list(names(enrichment_sub), !!metadata_path)
),
enrichment_sub_annot = target(
annotate_data(enrichment_sub, enrichment_annotations)
),
write_enrichment_sub_annot = target(
write_data(enrichment_sub_annot,
file_out(!!names.enrichment.sub.annot))
),
enrichment_annot = target(
dplyr::bind_rows(enrichment_sub_annot)
),
write_enrichment_annot = target(
write_data(enrichment_annot,
file_out(!!names.enrichment.pan.annot))
), # 18
# Enrichment Promax
enrichment_sub_promax = target(
compute_promax(enrichment_sub, enrichment_annotations)
),
write_enrichment_sub_promax = target(
write_data(enrichment_sub_promax,
file_out(!!names.enrichment.promax.sub))
),
enrichment_sub_promax_annot = target(
annotate_data(enrichment_sub_promax, enrichment_annotations)
),
write_enrichment_sub_promax_annot = target(
write_data(enrichment_sub_promax_annot,
file_out(!!names.enrichment.promax.sub.annot))
),
enrichment_promax = target(
dplyr::bind_rows(enrichment_sub_promax)
),
write_enrichment_promax = target(
write_data(enrichment_promax,
file_out(!!names.enrichment.promax.pan))
),
enrichment_promax_annot = target(
dplyr::bind_rows(enrichment_sub_promax_annot)
),
write_enrichment_promax_annot = target(
write_data(enrichment_promax_annot,
file_out(!!names.enrichment.promax.pan.annot))
), #26
)
}
if(runHits){
hits_plan <- drake::drake_plan(
# Hits
hits = target(
data.table::fread(file_in(!!hits_filename))
),
hits_sub = target(
split_data(hits)
# compute_hits(enrichment_sub, !!enrichment_threshold)
),
write_hits_sub = target(
write_data(hits_sub, file_out(!!names.hits.sub))
),
hits_sub_annot = target(
annotate_data(hits_sub, enrichment_annotations)
),
write_hits_sub_annot = target(
write_data(hits_sub_annot, file_out(!!names.hits.sub.annot))
),
# hits = target(
# dplyr::bind_rows(hits_sub)
# ),
write_hits = target(
write_data(hits, file_out(!!names.hits.pan))
),
hits_annot = target(
dplyr::bind_rows(hits_sub_annot)
),
write_hits_annot = target(
write_data(hits_annot, file_out(!!names.hits.pan.annot))
), #34
# Hits Prosum
hits_sub_prosum = target(
compute_prosum(hits_sub, enrichment_annotations)
),
write_hits_sub_prosum = target(
write_data(hits_sub_prosum, file_out(!!names.hits.sub.prosum))
),
hits_sub_prosum_annot = target(
annotate_data(hits_sub_prosum, enrichment_annotations)
),
write_hits_sub_prosum_annot = target(
write_data(hits_sub_prosum_annot, file_out(!!names.hits.sub.prosum.annot))
),
hits_prosum = target(
dplyr::bind_rows(hits_sub_prosum)
),
write_hits_prosum = target(
write_data(hits_prosum, file_out(!!names.hits.pan.prosum))
),
hits_prosum_annot = target(
dplyr::bind_rows(hits_sub_prosum_annot)
),
write_hits_prosum_annot = target(
write_data(hits_prosum_annot, file_out(!!names.hits.pan.prosum.annot))
),
# New Hits-Filtered Data Files
# hits_foldchange
hits_sub_foldchange = target(
emphasize_hit_data_list(foldchange_sub, hits_sub, 1)
),
write_hits_sub_foldchange = target(
write_data(hits_sub_foldchange, file_out(!!names.hits.foldchange.sub))
),
hits_sub_foldchange_annot = target(
annotate_data(hits_sub_foldchange, enrichment_annotations)
),
write_hits_sub_foldchange_annot = target(
write_data(hits_sub_foldchange_annot, file_out(!!names.hits.foldchange.sub.annot))
),
hits_foldchange = target(
dplyr::bind_rows(hits_sub_foldchange)
),
write_hits_foldchange = target(
write_data(hits_foldchange, file_out(!!names.hits.foldchange.pan))
),
hits_foldchange_annot = target(
dplyr::bind_rows(hits_sub_foldchange_annot)
),
write_hits_foldchange_annot = target(
write_data(hits_foldchange_annot, file_out(!!names.hits.foldchange.pan.annot))
),
# hits_foldchange promax
hits_sub_foldchange_promax = target(
compute_promax(hits_sub_foldchange, enrichment_annotations)
),
write_hits_sub_foldchange_promax = target(
write_data(hits_sub_foldchange_promax, file_out(!!names.hits.foldchange.sub.promax))
),
hits_sub_foldchange_promax_annot = target(
annotate_data(hits_sub_foldchange_promax, enrichment_annotations)
),
write_hits_sub_foldchange_promax_annot = target(
write_data(hits_sub_foldchange_promax_annot,
file_out(!!names.hits.foldchange.sub.promax.annot))
),
hits_foldchange_promax = target(
dplyr::bind_rows(hits_sub_foldchange_promax)
),
write_hits_foldchange_promax = target(
write_data(hits_foldchange_promax, file_out(!!names.hits.foldchange.pan.promax))
),
hits_foldchange_promax_annot = target(
dplyr::bind_rows(hits_sub_foldchange_promax_annot)
),
write_hits_foldchange_promax_annot = target(
write_data(hits_foldchange_promax_annot,
file_out(!!names.hits.foldchange.pan.promax.annot))
),
# hits_enrichment
hits_sub_enrichment = target(
emphasize_hit_data_list(enrichment_sub, hits_sub, 0)
),
write_hits_sub_enrichment = target(
write_data(hits_sub_enrichment, file_out(!!names.hits.enrichment.sub))
),
hits_sub_enrichment_annot = target(
annotate_data(hits_sub_enrichment, enrichment_annotations)
),
write_hits_sub_enrichment_annot = target(
write_data(hits_sub_enrichment_annot, file_out(!!names.hits.enrichment.sub.annot))
),
hits_enrichment = target(
dplyr::bind_rows(hits_sub_enrichment)
),
write_hits_enrichment = target(
write_data(hits_enrichment, file_out(!!names.hits.enrichment.pan))
),
hits_enrichment_annot = target(
dplyr::bind_rows(hits_sub_enrichment_annot)
),
write_hits_enrichment_annot = target(
write_data(hits_enrichment_annot, file_out(!!names.hits.enrichment.pan.annot))
),
# hits_enrichment promax
hits_sub_enrichment_promax = target(
compute_promax(hits_sub_enrichment, enrichment_annotations)
),
write_hits_sub_enrichment_promax = target(
write_data(hits_sub_enrichment_promax, file_out(!!names.hits.enrichment.sub.promax))
),
hits_sub_enrichment_promax_annot = target(
annotate_data(hits_sub_enrichment_promax, enrichment_annotations)
),
write_hits_sub_enrichment_promax_annot = target(
write_data(hits_sub_enrichment_promax_annot,
file_out(!!names.hits.enrichment.sub.promax.annot))
),
hits_enrichment_promax = target(
dplyr::bind_rows(hits_sub_enrichment_promax)
),
write_hits_enrichment_promax = target(
write_data(hits_enrichment_promax, file_out(!!names.hits.enrichment.pan.promax))
),
hits_enrichment_promax_annot = target(
dplyr::bind_rows(hits_sub_enrichment_promax_annot)
),
write_hits_enrichment_promax_annot = target(
write_data(hits_enrichment_promax_annot,
file_out(!!names.hits.enrichment.pan.promax.annot))
),
# hits_counts
hits_sub_counts = target(
emphasize_hit_data_list(counts_sub, hits_sub, 0)
),
write_hits_sub_counts = target(
write_data(hits_sub_counts, file_out(!!names.hits.counts.sub))
),
hits_sub_counts_annot = target(
annotate_data(hits_sub_counts, enrichment_annotations)
),
write_hits_sub_counts_annot = target(
write_data(hits_sub_counts_annot, file_out(!!names.hits.counts.sub.annot))
),
hits_counts = target(
dplyr::bind_rows(hits_sub_counts)
),
write_hits_counts = target(
write_data(hits_counts, file_out(!!names.hits.counts.pan))
),
hits_counts_annot = target(
dplyr::bind_rows(hits_sub_counts_annot)
),
write_hits_counts_annot = target(
write_data(hits_counts_annot, file_out(!!names.hits.counts.pan.annot))
)
)
}
if(runPolyclonal){
polyclonal_plan <- drake::drake_plan(
# Polyclonal
blast_pairs = target(
read_pairs_list(names(enrichment_sub), !!metadata_path)
),
polycl_sub = target(
compute_polycl(hits_sub, enrichment_annotations, blast_pairs)
),
write_polycl_sub = target(
write_data(polycl_sub, file_out(!!names.polycl.sub))
),
polycl_sub_annot = target(
annotate_data(polycl_sub, enrichment_annotations)
),
write_polycl_sub_annot = target(
write_data(polycl_sub_annot,
file_out(!!names.polycl.sub.annot))
),
polycl = target(
dplyr::bind_rows(polycl_sub)
),
write_polycl = target(
write_data(polycl, file_out(!!names.polycl.pan))
),
polycl_annot = target(
dplyr::bind_rows(polycl_sub_annot)
),
write_polycl_annot = target(
write_data(polycl_annot, file_out(!!names.polycl.pan.annot))
)
)
}
# --------------------------------------------------------------------------
# Fold Change
if(runFoldChange){
foldchange_plan <- drake::drake_plan(
foldchange = target(
data.table::fread(file_in(!!foldchange_filename))
), #10
write_foldchange = target(
write_data(foldchange, file_out(!!names.foldchange.pan))
),
foldchange_sub = target(
split_data(foldchange)
),
write_foldchange_sub = target(
write_data(foldchange_sub, file_out(!!names.foldchange.sub))
),
foldchange_annotations = target(
read_annot_list(names(foldchange_sub), !!metadata_path)
),
foldchange_sub_annot = target(
annotate_data(foldchange_sub, foldchange_annotations)
),
write_foldchange_sub_annot = target(
write_data(foldchange_sub_annot,
file_out(!!names.foldchange.sub.annot))
),
foldchange_annot = target(
dplyr::bind_rows(foldchange_sub_annot)
),
write_foldchange_annot = target(
write_data(foldchange_annot,
file_out(!!names.foldchange.pan.annot))
)
)
}
# --------------------------------------------------------------------------
# Counts
if(runCounts) {
counts_plan <- drake::drake_plan(
counts = data.table::fread(file_in(!!counts_filename)),
write_counts = target(
write_data(counts, file_out(!!names.counts.pan))
),
counts_sub = target(
split_data(counts)
),
write_counts_sub = target(
write_data(counts_sub, file_out(!!names.counts.sub))
),
counts_annotations = target(
# if(mean(counts_sub[[1]] == enrichment_sub[[1]]) == 1){
# enrichment_annotations
# } else{
read_annot_list(names(counts_sub), !!metadata_path)
# }
),
counts_sub_annot = target(
annotate_data(counts_sub, counts_annotations),
),
write_counts_sub_annot = target(
write_data(counts_sub_annot,
file_out(!!names.counts.sub.annot))
),
counts_annot = target(
dplyr::bind_rows(counts_sub_annot)
),
write_counts_annot = target(
write_data(counts_annot,
file_out(!!names.counts.pan.annot))
),
# Counts Prosum
counts_sub_prosum = target(
compute_prosum(counts_sub, counts_annotations)
),
write_counts_sub_prosum = target(
write_data(counts_sub_prosum,
file_out(!!names.counts.prosum.sub))
),
counts_sub_prosum_annot = target(
annotate_data(counts_sub_prosum, counts_annotations)
),
write_counts_sub_prosum_annot = target(
write_data(counts_sub_prosum_annot,
file_out(!!names.counts.prosum.sub.annot))
),
counts_prosum = target(
dplyr::bind_rows(counts_sub_prosum)
),
write_counts_prosum = target(
write_data(counts_prosum, file_out(!!names.counts.prosum.pan))
),
counts_prosum_annot = target(
dplyr::bind_rows(counts_sub_prosum_annot)
),
write_counts_prosum_annot = target(
write_data(counts_prosum_annot,
file_out(!!names.counts.prosum.pan.annot))
)
)
}
if(runAVARDA){
avpath <- "/data/hlarman1/PhIPdb/Software/AVARDA/"
avcase <- names.hits.avarda[grep("Virscan", names.hits.avarda)]
avdf <- paste0(avpath, "bin2/my_df.csv")
avtotal <- paste0(avpath, "bin2/total_probability_xr2.csv")
avpairwise <- paste0(avpath, "bin2/unique_probabilities3.csv")
avblast <- paste0(avpath, "bin2/VirScan_filtered_virus_blast_new.csv")
virdir <- e.libnames[grep("Virscan", e.libnames)]
avout <- paste0(virdir, "/AVARDA/")
if(!dir.exists(avout)) dir.create(avout)
AVARDA_plan <- drake::drake_plan(
hits_sub_avardanames = target(
prepare_avarda_names(hits_sub, enrichment_annotations)
),
write_hits_sub_avardanames = target(
write_data(hits_sub_avardanames,
file_out(!!names.hits.avarda))
),
command = target(
paste0("sbatch --export=case=",!!avcase,
# ",thresh=",!!enrichment_threshold,
",thresh=", "1",
",df=",!!avdf,
",total=",!!avtotal,
",pairwise=",!!avpairwise,
",blast=",!!avblast,
",out_path=",!!avout,
",out_name=",paste0(!!screen_name,"_"),
" ", !!avpath, "AVARDA_BMS.sh")
),
write_command = target(
writeLines(command, file_out("AVARDA_command.txt"))
),
runAVARDA = target(
{
file_in(!!names.hits.avarda)
system(command)
}
)
)
}
if(runEpitopefindr){
epitopefindr_plan <- drake::drake_plan(
# get panlibrary table of u_pep_id and pep_aa
annotation_merged_df = target(merge_annotations(enrichment_annotations)),
# for each patient assemble top 2k hits by foldchange
tryCatch(
run_epitopefindr = target(
{
if(!dir.exists("epitopefindr")) dir.create("epitopefindr")
if(!dir.exists("epitopefindr/temp")) dir.create("epitopefindr/temp")
run_epitopefindr(hits_foldchange, annotation_merged_df, epitopefindr_latex = TRUE, eth = e_t)
file_out("epitopefindr")
}
),
error = function(e) print(e)
)
)
}
if(runEpitopefindr_nolatex){
writeLines(as.character(e_thresh), "e_thresh.txt")
epitopefindr_plan <- drake::drake_plan(
e_t = as.numeric(readLines("e_thresh.txt")),
# get panlibrary table of u_pep_id and pep_aa
annotation_merged_df = target(merge_annotations(enrichment_annotations)),
# for each patient assemble top 2k hits by foldchange
run_epitopefindr = target(
{
if(!dir.exists("epitopefindr")) dir.create("epitopefindr")
if(!dir.exists("epitopefindr/temp")) dir.create("epitopefindr/temp")
run_epitopefindr(hits_foldchange, annotation_merged_df, epitopefindr_latex = FALSE, eth = e_t)
file_out("epitopefindr")
}
)
)
}
if(runPairwise){
#(!) todo
#convert pairs input.csv to samples.txt
#take input paths.txt (?)
# assemble counts with gather_samples
# call Daniel Pairwise to generate enrichments
# check if runenrichments. add those targetse.
# assemble plan below
}
#-------------
# setup main plan based on input parameters runCounts runEnrichment runAVARDA
main_plan <- params_plan
if(runCounts){main_plan %<>% rbind(counts_plan)}
if(runFoldChange){main_plan %<>% rbind(foldchange_plan)}
if(runEnrichment){main_plan %<>% rbind(enrichment_plan)}
if(runHits){main_plan %<>% rbind(hits_plan)}
if(runPolyclonal){main_plan %<>% rbind(polyclonal_plan)}
if(runAVARDA){main_plan %<>% rbind(AVARDA_plan)}
if(runEpitopefindr){main_plan %<>% rbind(epitopefindr_plan)}
if(runEpitopefindr_nolatex){main_plan %<>% rbind(epitopefindr_plan)}
return(main_plan)
}
brandonsie/phipmake documentation built on March 15, 2023, 3:24 p.m.
R Package Documentation
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Note that we can't provide technical support on individual packages. You should contact the package authors for that.
Defines functions define_plan
Documented in define_plan
#' Initialize and return drake_plan object. New for github drake 7.0+.
#'
#' @param params_path Path to project parameters file that can be created using the write_drake_params function.
#' @param runCounts Logical controlling whether or not to define counts targets.
#' @param runPairwise Logical controlling whether or not to define pairwise targets.
#' @param runFoldChange Logical controlling whether or not to define EdgeR fold change targets.
#' @param runEnrichment Logical controlling whether or not to define enrichment targets.
#' @param runPolyclonal Logical controlling whether or not to define enrichment targets.
#' @param runAVARDA Logical controlling whether or not to define AVARDA targets.
#' @param runEpitopefindr Logical controlling whether or not to run epitopefindr analysis on hits.
#' @param runEpitopefindr_nolatex Logical controlling whether or not to run epitopefindr analysis on hits without latex (replaces epitopefindr_latex).
#' @param e_thresh E value threshold for epitopefindr pairwise peptide sequence alignments. default 0.1.
#'
#' @export
#'
define_plan <- function(
params_path = "drake_params.tsv",
runCounts = TRUE,
runPairwise = FALSE,
runFoldChange = TRUE,
runEnrichment = TRUE,
runHits = TRUE,
runPolyclonal = TRUE,
runAVARDA = FALSE,
runEpitopefindr = FALSE,
runEpitopefindr_nolatex = FALSE,
e_thresh = 0.01
# epitopefindr_latex = FALSE
){
options(stringsAsFactors = FALSE)
# ============================================================================
# Settings
if(!file.exists(params_path)){
stop(paste("Params file missing.",
"If you haven't yet made a parameters file for this run,",
"try write_drake_params().",
"Curently looking for a parameters file named",
params_path, "in directory:", getwd()))
}
# Load parameters from drake_params.tsv
params <- data.table::fread(file_in(params_path))
# use_params <- c("screen_name", "counts_filename", "enrichment_filename",
# "enrichment_type", "enrichment_threshold", "metadata_path",
# "output_extension")
# for(i in 1:use_params){assign(i, getparam(params, i))}
screen_name <- getparam(params, "screen_name")
counts_filename <- getparam(params, "counts_filename")
counts_type <- getparam(params, "counts_type")
foldchange_filename <- getparam(params, "foldchange_filename")
foldchange_type <- getparam(params, "foldchange_type")
enrichment_filename <- getparam(params, "enrichment_filename")
enrichment_type <- getparam(params, "enrichment_type")
# enrichment_threshold <- getparam(params, "enrichment_threshold") %>% as.numeric
hits_filename <- getparam(params, "hits_filename")
metadata_path <- getparam(params, "metadata_path")
output_extension <- getparam(params, "output_extension")
output_separator <- getparam(params, "output_separator")
sublibrary_parallel <- as.logical(getparam(params, "sublibrary_parallel"))
# counts_libs <- getparam(params, "counts_libs")
# enrichment_libs <- getparam(params, "enrichment_libs")
# Establish sublibrary names
if(file.exists(counts_filename)){
temp.counts <- data.table::fread(counts_filename)
c.libs <- u_pep_id_to_libnames(temp.counts[,1])
c.lib.base <- c.libs[[2]]
c.libnames <- c.libs[[4]]
sn.lib.c <- paste0("_", c.libnames)
sn.libdir.c <- paste0(c.libnames, "/")
for(i in sn.libdir.c){if(!dir.exists(i)) dir.create(i)}
} else{
sn.lib.c <- sn.libdir.c <- "NA"
if(runCounts) {
warning(paste("Counts file is missing.",
"Are you in the right working directory?",
"Currently looking for a counts file named",
counts_filename, "in directory:", getwd()))
}
}
if(file.exists(enrichment_filename)){
temp.enrich <- data.table::fread(enrichment_filename)
e.libs <- u_pep_id_to_libnames(temp.enrich[,1])
e.lib.base <- e.libs[[2]]
e.libnames <- e.libs[[4]]
sn.lib.e <- paste0("_", e.libnames)
sn.libdir.e <- paste0(e.libnames, "/")
# Sublibrary directories create
for(i in sn.libdir.e){if(!dir.exists(i)) dir.create(i)
}
} else{
sn.lib.e <- sn.libdir.e <- "NA"
if(runEnrichment | runPolyclonal | runAVARDA){
warning(paste("Enrichment file is missing.",
"Are you in the right working directory?",
"Currently looking for an enrichment file named",
enrichment_filename, "in directory:", getwd()))
}
}
# ============================================================================
# Establish output file names
# ============================================================================
sn.ext <- paste0(".", output_extension)
sn.annot <- paste0("_annotated")
sn.a.ext <- paste0(sn.annot, sn.ext)
# Enrichment
sn.enrichment <- paste0(screen_name, "_", enrichment_type)
names.enrichment.pan <- paste0(sn.enrichment, sn.ext)
names.enrichment.pan.annot <- paste0(sn.enrichment, sn.a.ext)
sn.enrichment.sub <- paste0(sn.libdir.e, screen_name, sn.lib.e, "_", enrichment_type)
names.enrichment.sub <- paste0(sn.enrichment.sub, sn.ext)
names.enrichment.sub.annot <- paste0(sn.enrichment.sub, sn.a.ext)
# Promax
sn.enrichment.promax <- paste0(sn.enrichment, "_promax")
names.enrichment.promax.pan <- paste0(sn.enrichment.promax, sn.ext)
names.enrichment.promax.pan.annot <- paste0(sn.enrichment.promax, sn.a.ext)
sn.enrichment.promax.sub <- paste0(sn.libdir.e, screen_name, sn.lib.e, "_", enrichment_type, "_promax")
names.enrichment.promax.sub <- paste0(sn.enrichment.promax.sub, sn.ext)
names.enrichment.promax.sub.annot <- paste0(sn.enrichment.promax.sub, sn.a.ext)
# Hits
sn.hits <- paste0(screen_name, "_Hits")
names.hits.pan <- paste0(sn.hits, sn.ext)
names.hits.pan.annot <- paste0(sn.hits, sn.a.ext)
sn.hits.sub <- paste0(sn.libdir.e, screen_name, sn.lib.e, "_Hits")
names.hits.sub <- paste0(sn.hits.sub, sn.ext)
names.hits.sub.annot <- paste0(sn.hits.sub, sn.a.ext)
sn.hits.prosum <- paste0(sn.hits,"_prosum")
names.hits.pan.prosum <- paste0(sn.hits.prosum, sn.ext)
names.hits.pan.prosum.annot <- paste0(sn.hits.prosum, sn.a.ext)
sn.hits.prosum.sub <- paste0(sn.libdir.e, screen_name, sn.lib.e, "_Hits_prosum")
names.hits.sub.prosum <- paste0(sn.hits.prosum.sub, sn.ext)
names.hits.sub.prosum.annot <- paste0(sn.hits.prosum.sub, sn.a.ext)
sn.hits.foldchange.sub <- paste0(sn.hits.sub, "_foldchange")
names.hits.foldchange.sub <- paste0(sn.hits.foldchange.sub, sn.ext)
names.hits.foldchange.sub.annot <- paste0(sn.hits.foldchange.sub, sn.a.ext)
sn.hits.foldchange <- paste0(sn.hits, "_foldchange")
names.hits.foldchange.pan <- paste0(sn.hits.foldchange, sn.ext)
names.hits.foldchange.pan.annot <- paste0(sn.hits.foldchange, sn.a.ext)
sn.hits.foldchange.promax <- paste0(sn.hits.foldchange, "_promax")
names.hits.foldchange.pan.promax <- paste0(sn.hits.foldchange.promax, sn.ext)
names.hits.foldchange.pan.promax.annot <- paste0(sn.hits.foldchange.promax, sn.a.ext)
sn.hits.foldchange.promax.sub <- paste0(sn.hits.foldchange.sub, "_promax")
names.hits.foldchange.sub.promax <- paste0(sn.hits.foldchange.promax.sub, sn.ext)
names.hits.foldchange.sub.promax.annot <- paste0(sn.hits.foldchange.promax.sub, sn.a.ext)
sn.hits.enrichment.sub <- paste0(sn.hits.sub, "_enrichment")
names.hits.enrichment.sub <- paste0(sn.hits.enrichment.sub, sn.ext)
names.hits.enrichment.sub.annot <- paste0(sn.hits.enrichment.sub, sn.a.ext)
sn.hits.enrichment <- paste0(sn.hits, "_enrichment")
names.hits.enrichment.pan <- paste0(sn.hits.enrichment, sn.ext)
names.hits.enrichment.pan.annot <- paste0(sn.hits.enrichment, sn.a.ext)
sn.hits.enrichment.promax <- paste0(sn.hits.enrichment, "_promax")
names.hits.enrichment.pan.promax <- paste0(sn.hits.enrichment.promax, sn.ext)
names.hits.enrichment.pan.promax.annot <- paste0(sn.hits.enrichment.promax, sn.a.ext)
sn.hits.enrichment.promax.sub <- paste0(sn.hits.enrichment.sub, "_promax")
names.hits.enrichment.sub.promax <- paste0(sn.hits.enrichment.promax.sub, sn.ext)
names.hits.enrichment.sub.promax.annot <- paste0(sn.hits.enrichment.promax.sub, sn.a.ext)
sn.hits.counts.sub <- paste0(sn.hits.sub, "_counts")
names.hits.counts.sub <- paste0(sn.hits.counts.sub, sn.ext)
names.hits.counts.sub.annot <- paste0(sn.hits.counts.sub, sn.a.ext)
sn.hits.counts <- paste0(sn.hits, "_counts")
names.hits.counts.pan <- paste0(sn.hits.counts, sn.ext)
names.hits.counts.pan.annot <- paste0(sn.hits.counts, sn.a.ext)
# Polyclonal
sn.polycl <- paste0(screen_name, "_Polyclonal")
names.polycl.pan <- paste0(sn.polycl, sn.ext)
names.polycl.pan.annot <- paste0(sn.polycl, sn.a.ext)
sn.polycl.sub <- paste0(sn.libdir.e, screen_name, sn.lib.e, "_Polyclonal")
names.polycl.sub <- paste0(sn.polycl.sub, sn.ext)
names.polycl.sub.annot <- paste0(sn.polycl.sub, sn.a.ext)
# Counts
sn.counts <- paste0(screen_name, "_", counts_type)
names.counts.pan <- paste0(sn.counts, sn.ext)
names.counts.pan.annot <- paste0(sn.counts, sn.a.ext)
sn.counts.sub <- paste0(sn.libdir.c, screen_name, sn.lib.c, "_", counts_type)
names.counts.sub <- paste0(sn.counts.sub, sn.ext)
names.counts.sub.annot <- paste0(sn.counts.sub, sn.a.ext)
sn.counts.prosum <- paste0(sn.counts, "_prosum")
names.counts.prosum.pan <- paste0(sn.counts.prosum, sn.ext)
names.counts.prosum.pan.annot <- paste0(sn.counts.prosum, sn.a.ext)
sn.counts.prosum.sub <- paste0(sn.libdir.c, screen_name, sn.lib.c, "_", counts_type, "_prosum")
names.counts.prosum.sub <- paste0(sn.counts.prosum.sub, sn.ext)
names.counts.prosum.sub.annot <- paste0(sn.counts.prosum.sub, sn.a.ext)
# AVARDA
names.enrichment.avarda <- paste0(sn.enrichment.sub,
"_avardanames", sn.ext)
names.hits.avarda <- paste0(sn.hits.sub,
"_avardanames", sn.ext)
# Fold Change
sn.foldchange <- paste0(screen_name, "_", foldchange_type)
names.foldchange.pan <- paste0(sn.foldchange, sn.ext)
names.foldchange.pan.annot <- paste0(sn.foldchange, sn.a.ext)
sn.foldchange.sub <- paste0(sn.libdir.e, screen_name, sn.lib.e, "_", foldchange_type)
names.foldchange.sub <- paste0(sn.foldchange.sub, sn.ext)
names.foldchange.sub.annot <- paste0(sn.foldchange.sub, sn.a.ext)
# ============================================================================
# Plans
# --------------------------------------------------------------------------
# Parameters
# --------------------------------------------------------------------------
params_plan <- drake::drake_plan(
# Load parameters in plan environment
params = data.table::fread(file_in("drake_params.tsv")),
screen_name = getparam(params, "screen_name"),
counts_filename = getparam(params, "counts_filename"),
counts_type = getparam(params, "counts_type"),
enrichment_filename = getparam(params, "enrichment_filename"),
enrichment_type = getparam(params, "enrichment_type"),
# enrichment_threshold = getparam(params, "enrichment_threshold") %>% as.numeric,
hits_filename = getparam(params, "hits_filename"),
metadata_path = getparam(params, "metadata_path"),
output_extension = getparam(params, "output_extension"),
output_separator = getparam(params, "output_separator"),
sublibrary_parallel = as.logical(getparam(params, "sublibrary_parallel"))
)
# --------------------------------------------------------------------------
# Enrichment
if(runEnrichment) {
enrichment_plan <- drake::drake_plan(
enrichment = target(
data.table::fread(file_in(!!enrichment_filename))
), #10
write_enrichment = target(
write_data(enrichment, file_out(!!names.enrichment.pan))
),
enrichment_sub = target(
split_data(enrichment)
),
write_enrichment_sub = target(
write_data(enrichment_sub, file_out(!!names.enrichment.sub))
),
enrichment_annotations = target(
read_annot_list(names(enrichment_sub), !!metadata_path)
),
enrichment_sub_annot = target(
annotate_data(enrichment_sub, enrichment_annotations)
),
write_enrichment_sub_annot = target(
write_data(enrichment_sub_annot,
file_out(!!names.enrichment.sub.annot))
),
enrichment_annot = target(
dplyr::bind_rows(enrichment_sub_annot)
),
write_enrichment_annot = target(
write_data(enrichment_annot,
file_out(!!names.enrichment.pan.annot))
), # 18
# Enrichment Promax
enrichment_sub_promax = target(
compute_promax(enrichment_sub, enrichment_annotations)
),
write_enrichment_sub_promax = target(
write_data(enrichment_sub_promax,
file_out(!!names.enrichment.promax.sub))
),
enrichment_sub_promax_annot = target(
annotate_data(enrichment_sub_promax, enrichment_annotations)
),
write_enrichment_sub_promax_annot = target(
write_data(enrichment_sub_promax_annot,
file_out(!!names.enrichment.promax.sub.annot))
),
enrichment_promax = target(
dplyr::bind_rows(enrichment_sub_promax)
),
write_enrichment_promax = target(
write_data(enrichment_promax,
file_out(!!names.enrichment.promax.pan))
),
enrichment_promax_annot = target(
dplyr::bind_rows(enrichment_sub_promax_annot)
),
write_enrichment_promax_annot = target(
write_data(enrichment_promax_annot,
file_out(!!names.enrichment.promax.pan.annot))
), #26
)
}
if(runHits){
hits_plan <- drake::drake_plan(
# Hits
hits = target(
data.table::fread(file_in(!!hits_filename))
),
hits_sub = target(
split_data(hits)
# compute_hits(enrichment_sub, !!enrichment_threshold)
),
write_hits_sub = target(
write_data(hits_sub, file_out(!!names.hits.sub))
),
hits_sub_annot = target(
annotate_data(hits_sub, enrichment_annotations)
),
write_hits_sub_annot = target(
write_data(hits_sub_annot, file_out(!!names.hits.sub.annot))
),
# hits = target(
# dplyr::bind_rows(hits_sub)
# ),
write_hits = target(
write_data(hits, file_out(!!names.hits.pan))
),
hits_annot = target(
dplyr::bind_rows(hits_sub_annot)
),
write_hits_annot = target(
write_data(hits_annot, file_out(!!names.hits.pan.annot))
), #34
# Hits Prosum
hits_sub_prosum = target(
compute_prosum(hits_sub, enrichment_annotations)
),
write_hits_sub_prosum = target(
write_data(hits_sub_prosum, file_out(!!names.hits.sub.prosum))
),
hits_sub_prosum_annot = target(
annotate_data(hits_sub_prosum, enrichment_annotations)
),
write_hits_sub_prosum_annot = target(
write_data(hits_sub_prosum_annot, file_out(!!names.hits.sub.prosum.annot))
),
hits_prosum = target(
dplyr::bind_rows(hits_sub_prosum)
),
write_hits_prosum = target(
write_data(hits_prosum, file_out(!!names.hits.pan.prosum))
),
hits_prosum_annot = target(
dplyr::bind_rows(hits_sub_prosum_annot)
),
write_hits_prosum_annot = target(
write_data(hits_prosum_annot, file_out(!!names.hits.pan.prosum.annot))
),
# New Hits-Filtered Data Files
# hits_foldchange
hits_sub_foldchange = target(
emphasize_hit_data_list(foldchange_sub, hits_sub, 1)
),
write_hits_sub_foldchange = target(
write_data(hits_sub_foldchange, file_out(!!names.hits.foldchange.sub))
),
hits_sub_foldchange_annot = target(
annotate_data(hits_sub_foldchange, enrichment_annotations)
),
write_hits_sub_foldchange_annot = target(
write_data(hits_sub_foldchange_annot, file_out(!!names.hits.foldchange.sub.annot))
),
hits_foldchange = target(
dplyr::bind_rows(hits_sub_foldchange)
),
write_hits_foldchange = target(
write_data(hits_foldchange, file_out(!!names.hits.foldchange.pan))
),
hits_foldchange_annot = target(
dplyr::bind_rows(hits_sub_foldchange_annot)
),
write_hits_foldchange_annot = target(
write_data(hits_foldchange_annot, file_out(!!names.hits.foldchange.pan.annot))
),
# hits_foldchange promax
hits_sub_foldchange_promax = target(
compute_promax(hits_sub_foldchange, enrichment_annotations)
),
write_hits_sub_foldchange_promax = target(
write_data(hits_sub_foldchange_promax, file_out(!!names.hits.foldchange.sub.promax))
),
hits_sub_foldchange_promax_annot = target(
annotate_data(hits_sub_foldchange_promax, enrichment_annotations)
),
write_hits_sub_foldchange_promax_annot = target(
write_data(hits_sub_foldchange_promax_annot,
file_out(!!names.hits.foldchange.sub.promax.annot))
),
hits_foldchange_promax = target(
dplyr::bind_rows(hits_sub_foldchange_promax)
),
write_hits_foldchange_promax = target(
write_data(hits_foldchange_promax, file_out(!!names.hits.foldchange.pan.promax))
),
hits_foldchange_promax_annot = target(
dplyr::bind_rows(hits_sub_foldchange_promax_annot)
),
write_hits_foldchange_promax_annot = target(
write_data(hits_foldchange_promax_annot,
file_out(!!names.hits.foldchange.pan.promax.annot))
),
# hits_enrichment
hits_sub_enrichment = target(
emphasize_hit_data_list(enrichment_sub, hits_sub, 0)
),
write_hits_sub_enrichment = target(
write_data(hits_sub_enrichment, file_out(!!names.hits.enrichment.sub))
),
hits_sub_enrichment_annot = target(
annotate_data(hits_sub_enrichment, enrichment_annotations)
),
write_hits_sub_enrichment_annot = target(
write_data(hits_sub_enrichment_annot, file_out(!!names.hits.enrichment.sub.annot))
),
hits_enrichment = target(
dplyr::bind_rows(hits_sub_enrichment)
),
write_hits_enrichment = target(
write_data(hits_enrichment, file_out(!!names.hits.enrichment.pan))
),
hits_enrichment_annot = target(
dplyr::bind_rows(hits_sub_enrichment_annot)
),
write_hits_enrichment_annot = target(
write_data(hits_enrichment_annot, file_out(!!names.hits.enrichment.pan.annot))
),
# hits_enrichment promax
hits_sub_enrichment_promax = target(
compute_promax(hits_sub_enrichment, enrichment_annotations)
),
write_hits_sub_enrichment_promax = target(
write_data(hits_sub_enrichment_promax, file_out(!!names.hits.enrichment.sub.promax))
),
hits_sub_enrichment_promax_annot = target(
annotate_data(hits_sub_enrichment_promax, enrichment_annotations)
),
write_hits_sub_enrichment_promax_annot = target(
write_data(hits_sub_enrichment_promax_annot,
file_out(!!names.hits.enrichment.sub.promax.annot))
),
hits_enrichment_promax = target(
dplyr::bind_rows(hits_sub_enrichment_promax)
),
write_hits_enrichment_promax = target(
write_data(hits_enrichment_promax, file_out(!!names.hits.enrichment.pan.promax))
),
hits_enrichment_promax_annot = target(
dplyr::bind_rows(hits_sub_enrichment_promax_annot)
),
write_hits_enrichment_promax_annot = target(
write_data(hits_enrichment_promax_annot,
file_out(!!names.hits.enrichment.pan.promax.annot))
),
# hits_counts
hits_sub_counts = target(
emphasize_hit_data_list(counts_sub, hits_sub, 0)
),
write_hits_sub_counts = target(
write_data(hits_sub_counts, file_out(!!names.hits.counts.sub))
),
hits_sub_counts_annot = target(
annotate_data(hits_sub_counts, enrichment_annotations)
),
write_hits_sub_counts_annot = target(
write_data(hits_sub_counts_annot, file_out(!!names.hits.counts.sub.annot))
),
hits_counts = target(
dplyr::bind_rows(hits_sub_counts)
),
write_hits_counts = target(
write_data(hits_counts, file_out(!!names.hits.counts.pan))
),
hits_counts_annot = target(
dplyr::bind_rows(hits_sub_counts_annot)
),
write_hits_counts_annot = target(
write_data(hits_counts_annot, file_out(!!names.hits.counts.pan.annot))
)
)
}
if(runPolyclonal){
polyclonal_plan <- drake::drake_plan(
# Polyclonal
blast_pairs = target(
read_pairs_list(names(enrichment_sub), !!metadata_path)
),
polycl_sub = target(
compute_polycl(hits_sub, enrichment_annotations, blast_pairs)
),
write_polycl_sub = target(
write_data(polycl_sub, file_out(!!names.polycl.sub))
),
polycl_sub_annot = target(
annotate_data(polycl_sub, enrichment_annotations)
),
write_polycl_sub_annot = target(
write_data(polycl_sub_annot,
file_out(!!names.polycl.sub.annot))
),
polycl = target(
dplyr::bind_rows(polycl_sub)
),
write_polycl = target(
write_data(polycl, file_out(!!names.polycl.pan))
),
polycl_annot = target(
dplyr::bind_rows(polycl_sub_annot)
),
write_polycl_annot = target(
write_data(polycl_annot, file_out(!!names.polycl.pan.annot))
)
)
}
# --------------------------------------------------------------------------
# Fold Change
if(runFoldChange){
foldchange_plan <- drake::drake_plan(
foldchange = target(
data.table::fread(file_in(!!foldchange_filename))
), #10
write_foldchange = target(
write_data(foldchange, file_out(!!names.foldchange.pan))
),
foldchange_sub = target(
split_data(foldchange)
),
write_foldchange_sub = target(
write_data(foldchange_sub, file_out(!!names.foldchange.sub))
),
foldchange_annotations = target(
read_annot_list(names(foldchange_sub), !!metadata_path)
),
foldchange_sub_annot = target(
annotate_data(foldchange_sub, foldchange_annotations)
),
write_foldchange_sub_annot = target(
write_data(foldchange_sub_annot,
file_out(!!names.foldchange.sub.annot))
),
foldchange_annot = target(
dplyr::bind_rows(foldchange_sub_annot)
),
write_foldchange_annot = target(
write_data(foldchange_annot,
file_out(!!names.foldchange.pan.annot))
)
)
}
# --------------------------------------------------------------------------
# Counts
if(runCounts) {
counts_plan <- drake::drake_plan(
counts = data.table::fread(file_in(!!counts_filename)),
write_counts = target(
write_data(counts, file_out(!!names.counts.pan))
),
counts_sub = target(
split_data(counts)
),
write_counts_sub = target(
write_data(counts_sub, file_out(!!names.counts.sub))
),
counts_annotations = target(
# if(mean(counts_sub[[1]] == enrichment_sub[[1]]) == 1){
# enrichment_annotations
# } else{
read_annot_list(names(counts_sub), !!metadata_path)
# }
),
counts_sub_annot = target(
annotate_data(counts_sub, counts_annotations),
),
write_counts_sub_annot = target(
write_data(counts_sub_annot,
file_out(!!names.counts.sub.annot))
),
counts_annot = target(
dplyr::bind_rows(counts_sub_annot)
),
write_counts_annot = target(
write_data(counts_annot,
file_out(!!names.counts.pan.annot))
),
# Counts Prosum
counts_sub_prosum = target(
compute_prosum(counts_sub, counts_annotations)
),
write_counts_sub_prosum = target(
write_data(counts_sub_prosum,
file_out(!!names.counts.prosum.sub))
),
counts_sub_prosum_annot = target(
annotate_data(counts_sub_prosum, counts_annotations)
),
write_counts_sub_prosum_annot = target(
write_data(counts_sub_prosum_annot,
file_out(!!names.counts.prosum.sub.annot))
),
counts_prosum = target(
dplyr::bind_rows(counts_sub_prosum)
),
write_counts_prosum = target(
write_data(counts_prosum, file_out(!!names.counts.prosum.pan))
),
counts_prosum_annot = target(
dplyr::bind_rows(counts_sub_prosum_annot)
),
write_counts_prosum_annot = target(
write_data(counts_prosum_annot,
file_out(!!names.counts.prosum.pan.annot))
)
)
}
if(runAVARDA){
avpath <- "/data/hlarman1/PhIPdb/Software/AVARDA/"
avcase <- names.hits.avarda[grep("Virscan", names.hits.avarda)]
avdf <- paste0(avpath, "bin2/my_df.csv")
avtotal <- paste0(avpath, "bin2/total_probability_xr2.csv")
avpairwise <- paste0(avpath, "bin2/unique_probabilities3.csv")
avblast <- paste0(avpath, "bin2/VirScan_filtered_virus_blast_new.csv")
virdir <- e.libnames[grep("Virscan", e.libnames)]
avout <- paste0(virdir, "/AVARDA/")
if(!dir.exists(avout)) dir.create(avout)
AVARDA_plan <- drake::drake_plan(
hits_sub_avardanames = target(
prepare_avarda_names(hits_sub, enrichment_annotations)
),
write_hits_sub_avardanames = target(
write_data(hits_sub_avardanames,
file_out(!!names.hits.avarda))
),
command = target(
paste0("sbatch --export=case=",!!avcase,
# ",thresh=",!!enrichment_threshold,
",thresh=", "1",
",df=",!!avdf,
",total=",!!avtotal,
",pairwise=",!!avpairwise,
",blast=",!!avblast,
",out_path=",!!avout,
",out_name=",paste0(!!screen_name,"_"),
" ", !!avpath, "AVARDA_BMS.sh")
),
write_command = target(
writeLines(command, file_out("AVARDA_command.txt"))
),
runAVARDA = target(
{
file_in(!!names.hits.avarda)
system(command)
}
)
)
}
if(runEpitopefindr){
epitopefindr_plan <- drake::drake_plan(
# get panlibrary table of u_pep_id and pep_aa
annotation_merged_df = target(merge_annotations(enrichment_annotations)),
# for each patient assemble top 2k hits by foldchange
tryCatch(
run_epitopefindr = target(
{
if(!dir.exists("epitopefindr")) dir.create("epitopefindr")
if(!dir.exists("epitopefindr/temp")) dir.create("epitopefindr/temp")
run_epitopefindr(hits_foldchange, annotation_merged_df, epitopefindr_latex = TRUE, eth = e_t)
file_out("epitopefindr")
}
),
error = function(e) print(e)
)
)
}
if(runEpitopefindr_nolatex){
writeLines(as.character(e_thresh), "e_thresh.txt")
epitopefindr_plan <- drake::drake_plan(
e_t = as.numeric(readLines("e_thresh.txt")),
# get panlibrary table of u_pep_id and pep_aa
annotation_merged_df = target(merge_annotations(enrichment_annotations)),
# for each patient assemble top 2k hits by foldchange
run_epitopefindr = target(
{
if(!dir.exists("epitopefindr")) dir.create("epitopefindr")
if(!dir.exists("epitopefindr/temp")) dir.create("epitopefindr/temp")
run_epitopefindr(hits_foldchange, annotation_merged_df, epitopefindr_latex = FALSE, eth = e_t)
file_out("epitopefindr")
}
)
)
}
if(runPairwise){
#(!) todo
#convert pairs input.csv to samples.txt
#take input paths.txt (?)
# assemble counts with gather_samples
# call Daniel Pairwise to generate enrichments
# check if runenrichments. add those targetse.
# assemble plan below
}
#-------------
# setup main plan based on input parameters runCounts runEnrichment runAVARDA
main_plan <- params_plan
if(runCounts){main_plan %<>% rbind(counts_plan)}
if(runFoldChange){main_plan %<>% rbind(foldchange_plan)}
if(runEnrichment){main_plan %<>% rbind(enrichment_plan)}
if(runHits){main_plan %<>% rbind(hits_plan)}
if(runPolyclonal){main_plan %<>% rbind(polyclonal_plan)}
if(runAVARDA){main_plan %<>% rbind(AVARDA_plan)}
if(runEpitopefindr){main_plan %<>% rbind(epitopefindr_plan)}
if(runEpitopefindr_nolatex){main_plan %<>% rbind(epitopefindr_plan)}
return(main_plan)
}
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