biopipen 0.33.1__py3-none-any.whl → 0.34.0__py3-none-any.whl

biopipen/scripts/misc/Plot.R

@@ -0,0 +1,80 @@
+library(gglogger)
+library(plotthis)
+library(rlang)
+library(biopipen.utils)
+
+datafile <- {{in.datafile | r}}
+plotfile <- {{out.plotfile | r}}
+plotprefix <- {{out.plotfile | prefix | r}}
+read_opts <- {{envs.read_opts | r: todot="-"}}
+envs <- {{envs | r}}
+
+fn <- envs$fn
+envs$fn <- NULL
+devpars <- envs$devpars
+envs$devpars <- NULL
+more_formats <- envs$more_formats
+envs$more_formats <- NULL
+save_code <- envs$save_code
+envs$save_code <- NULL
+envs$read_opts <- NULL
+
+if (endsWith(datafile, ".qs") || endsWith(datafile, ".qs2") ||
+    endsWith(datafile, ".rds") || endsWith(datafile, ".RDS")) {
+    envs$data <- read_obj(datafile)
+} else {
+    read_opts <- read_opts %||% list()
+    read_opts$file <- datafile
+    envs$data <- do.call(read.table, read_opts)
+}
+
+if (fn == "ManhattanPlot" && !is.null(envs$chromosomes)) {
+    norm_chroms <- function(chrs) {
+        chrs <- as.character(chrs)
+        if (length(chrs) == 1 && grepl(",", chrs)) {
+            chrs <- trimws(unlist(strsplit(chrs, ",")))
+        }
+        if (length(chrs) > 1) {
+            return(unique(unlist(sapply(chrs, function(chr) norm_chroms(chr)))))
+        }
+        if (!grepl("-", chrs)) { return(chrs) }
+
+        # expand chr1-22 -> chr1, chr2, ..., chr22
+        # chr1-22 -> 'chr1', '22'
+        chrs <- unlist(strsplit(chrs, "-"))
+        if (length(chrs) != 2) {
+            stop(paste0("Invalid chroms: ", chrs))
+        }
+        # detect prefix
+        prefix1 <- gsub("[0-9]", "", chrs[1])
+        prefix2 <- gsub("[0-9]", "", chrs[2])
+        if (nchar(prefix2) > 0 && prefix1 != prefix2) {
+            stop(paste0("Invalid chroms: ", chrs, " (prefix mismatch)"))
+        }
+        chr_a <- as.integer(substring(chrs[1], nchar(prefix1) + 1))
+        chr_b <- as.integer(substring(chrs[2], nchar(prefix2) + 1))
+        chr_min <- min(chr_a, chr_b)
+        chr_max <- max(chr_a, chr_b)
+        return(paste0(prefix1, chr_min:chr_max))
+    }
+
+    envs$chromosomes <- norm_chroms(envs$chromosomes)
+}
+
+plotfn <- utils::getFromNamespace(fn, "plotthis")
+if (save_code) {
+    plotfn <- gglogger::register(plotfn, name = fn)
+}
+
+p <- do_call(plotfn, envs)
+save_plot(p, plotprefix, devpars, formats = unique(c("png", more_formats)))
+
+if (save_code) {
+    save_plotcode(
+        p,
+        setup = c('library(plotthis)', '', 'load("data.RData")', 'list2env(envs, envir = .GlobalEnv)'),
+        prefix = plotprefix,
+        "envs",
+        auto_data_setup = FALSE
+    )
+}

biopipen/scripts/plot/VennDiagram.R

@@ -1,8 +1,8 @@
 {{ biopipen_dir | joinpaths: "utils", "io.R" | source_r }}
 {{ biopipen_dir | joinpaths: "utils", "plot.R" | source_r }}
 
-infile = {{in.infile | quote}}
-outfile = {{out.outfile | quote}}
+infile = {{in.infile | r}}
+outfile = {{out.outfile | r}}
 inopts = {{envs.inopts | r}}
 intype = {{envs.intype | r}}
 devpars = {{envs.devpars | r}}

biopipen/scripts/protein/ProdigySummary.R

@@ -1,11 +1,7 @@
-{{ biopipen_dir | joinpaths: "utils", "misc.R" | source_r }}
-
 library(rlang)
 library(dplyr)
-library(ggplot2)
-library(ggprism)
-
-theme_set(theme_prism())
+library(biopipen.utils)
+library(plotthis)
 
 infiles <- {{in.infiles | r}}
 outdir <- {{out.outdir | r}}
@@ -24,12 +20,15 @@ if (is.character(group)) {
     stop(paste0("Invalid group: ", paste0(group, collapse = ", ")))
 }
 
-log_info("Reading and merging metrics for each sample ...")
+log <- get_logger()
+reporter <- get_reporter()
+
+log$info("Reading and merging metrics for each sample ...")
 metrics <- NULL
 
 for (infile in infiles) {
     sample <- sub("_prodigy$", "", basename(dirname(infile)))
-    log_debug("- Reading metrics from {sample}")
+    log$debug("- Reading metrics from {sample}")
     metric <- read.table(
         infile,
         header = TRUE,
@@ -55,7 +54,7 @@ write.table(
     row.names = FALSE
 )
 
-add_report(
+reporter$add(
     list(kind = "descr", content = "Metrics for all samples"),
     list(kind = "table", src = file.path(outdir, "metrics.txt")),
     h1 = "Metrics of all samples"
@@ -76,17 +75,17 @@ METRIC_DESCR = list(
 )
 
 if (!is.null(group)) {
-    log_info("Merging group information ...")
+    log$info("Merging group information ...")
     metrics <- group %>%
         left_join(metrics, by = "Sample") %>%
         mutate(Group = factor(Group, levels = unique(Group)))
 }
 
-log_info("Plotting Prodigy metrics ...")
+log$info("Plotting Prodigy metrics ...")
 for (metric in names(METRIC_DESCR)) {
-    log_info("- {metric}: {METRIC_DESCR[[metric]]}")
+    log$info("- {metric}: {METRIC_DESCR[[metric]]}")
 
-    add_report(
+    reporter$add(
         list(
             kind = "descr",
             content = METRIC_DESCR[[metric]] %||% paste0("Metric: ", metric)
@@ -94,18 +93,22 @@ for (metric in names(METRIC_DESCR)) {
         h1 = metric
     )
 
-    # barplot
-    p <- ggplot(metrics, aes(x = Sample, y = !!sym(metric))) +
-        geom_bar(stat = "identity", fill = "steelblue") +
-        labs(x = "Sample", y = metric) +
-        theme(axis.text.x = element_text(angle = 90, hjust = 1))
+    p <- plotthis::BarPlot(
+        x = "Sample",
+        y = metric,
+        x_text_angle = 90,
+        fill = "Group",
+        data = metrics
+    )
 
     figfile <- file.path(outdir, paste0(slugify(metric), ".barplot.png"))
-    png(figfile, height = 600, res = 100, width = nrow(metrics) * 30 + 200)
+    height <- attr(p, "height") %||% 6
+    width <- attr(p, "width") %||% (nrow(metrics) * .3 + 2)
+    png(figfile, height = height * 100, res = 100, width = width * 100)
     print(p)
     dev.off()
 
-    add_report(
+    reporter$add(
         list(src = figfile, name = "By Sample"),
         ui = "table_of_images",
         h1 = metric
@@ -113,21 +116,25 @@ for (metric in names(METRIC_DESCR)) {
 
     if (is.null(group)) { next }
     # group: Sample, Group
-    p <- ggplot(metrics, aes(x = Group, y = !!sym(metric))) +
-        geom_boxplot(fill = "steelblue") +
-        labs(x = "Group", y = metric) +
-        theme(axis.text.x = element_text(angle = 90, hjust = 1))
+    p <- plotthis::BarPlot(
+        data = metrics,
+        x = "Group",
+        y = metric,
+        x_text_angle = 90
+    )
 
     figfile <- file.path(outdir, paste0(slugify(metric), ".boxplot.png"))
-    png(figfile, height = 600, res = 100, width = length(unique(metrics$Group)) * 30 + 200)
+    height <- attr(p, "height") %||% 6
+    width <- attr(p, "width") %||% (length(unique(metrics$Group)) * 0.3 + 2)
+    png(figfile, height = height * 100, res = 100, width = width * 100)
     print(p)
     dev.off()
 
-    add_report(
+    reporter$add(
         list(src = figfile, name = "By Group"),
         ui = "table_of_images",
         h1 = metric
     )
 }
 
-save_report(joboutdir)
+reporter$save(joboutdir)

biopipen/scripts/regulatory/MotifAffinityTest.R

@@ -1,9 +1,9 @@
 # Script for regulatory.MotifAffinityTest
-{{ biopipen_dir | joinpaths: "utils", "misc.R" | source_r }}
-{{ biopipen_dir | joinpaths: "scripts", "regulatory", "motifs-common.R" | source_r }}
+{% include biopipen_dir + "/scripts/regulatory/motifs-common.R" %}
 
 library(BiocParallel)
 library(BSgenome)
+library(biopipen.utils)
 
 motiffile <- {{in.motiffile | r}}
 varfile <- {{in.varfile | r}}
@@ -42,16 +42,18 @@ if (is.null(motif_col) && is.null(regulator_col)) {
     stop("Either motif (envs.motif_col) or regulator (envs.regulator_col) column must be provided")
 }
 
-log_info("Reading input regulator/motif file ...")
+log <- get_logger()
+
+log$info("Reading input regulator/motif file ...")
 in_motifs <- read.table(motiffile, header=TRUE, sep="\t", stringsAsFactors=FALSE, check.names = FALSE)
 
-log_info("Ensuring motifs and regulators in the input data ...")
+log$info("Ensuring motifs and regulators in the input data ...")
 in_motifs <- ensure_regulator_motifs(in_motifs, outdir, motif_col, regulator_col, regmotifs, notfound = notfound)
 genome_pkg <- get_genome_pkg(genome)
 
-log_info("Reading variant file ...")
+log$info("Reading variant file ...")
 if (grepl("\\.vcf$", varfile) || grepl("\\.vcf\\.gz$", varfile)) {
-    log_info("Converting VCF file to BED file ...")
+    log$info("Converting VCF file to BED file ...")
     varfile_bed <- file.path(outdir, gsub("\\.vcf(\\.gz)?$", ".bed", basename(varfile)))
     cmd <- c(
         bcftools, "query",
@@ -69,7 +71,7 @@ if (grepl("\\.vcf$", varfile) || grepl("\\.vcf\\.gz$", varfile)) {
 snpinfo <- read.table(varfile, header=FALSE, stringsAsFactors=FALSE)
 colnames(snpinfo) <- c("chrom", "start", "end", "name", "score", "strand", "ref", "alt")
 
-log_info("Reading motif database ...")
+log$info("Reading motif database ...")
 mdb <- read_meme_to_motifdb(motifdb, in_motifs, motif_col, regulator_col, notfound, outdir)
 
 tool <- tolower(tool)
@@ -77,8 +79,8 @@ tool <- match.arg(tool, c("motifbreakr", "atsnp"))
 
 if (tool == "motifbreakr") {
     motifbreakr_args <- {{envs.motifbreakr_args | r}}
-    {{ biopipen_dir | joinpaths: "scripts", "regulatory", "MotifAffinityTest_MotifBreakR.R" | source_r }}
+    {% include biopipen_dir + "/scripts/regulatory/MotifAffinityTest_MotifBreakR.R" %}
 } else {  # atsnp
     atsnp_args <- {{envs.atsnp_args | r}}
-    {{ biopipen_dir | joinpaths: "scripts", "regulatory", "MotifAffinityTest_AtSNP.R" | source_r }}
+    {% include biopipen_dir + "/scripts/regulatory/MotifAffinityTest_AtSNP.R" %}
 }

biopipen/scripts/regulatory/MotifAffinityTest_AtSNP.R

@@ -1,7 +1,7 @@
 library(atSNP)
 library(rtracklayer)
 
-log_info("Converting snpinfo to atSNP object ...")
+log$info("Converting snpinfo to atSNP object ...")
 
 # c("chrom", "start", "end", "name", "score", "strand", "ref", "alt", "ref_seq", "alt_seq")
 if (any(nchar(snpinfo$ref) != 1) || any(nchar(snpinfo$alt) != 1)) {
@@ -34,10 +34,10 @@ snps <- LoadSNPData(
     half.window.size = k
 )
 
-log_info("Running atSNP ...")
+log$info("Running atSNP ...")
 atsnp_scores <- ComputeMotifScore(motif_lib, snps, ncores = ncores)
 
-log_info("Calculating p values ...")
+log$info("Calculating p values ...")
 atsnp_result <- ComputePValues(
     motif.lib = motif_lib,
     snp.info = snps,
@@ -85,7 +85,7 @@ write.table(
     sep = "\t", quote = FALSE, row.names = FALSE
 )
 
-log_info("Plotting variants ...")
+log$info("Plotting variants ...")
 # Convert result to GRanges object
 atsnp_result$alleleDiff <- -atsnp_result[[cutoff_col]]
 atsnp_result$effect <- "strong"
@@ -103,7 +103,7 @@ if (is.null(plots) || length(plots) == 0) {
     variants <- names(plots)
 }
 for (variant in variants) {
-    log_info("- Variant: {variant}")
+    log$info("- Variant: {variant}")
     if (is.null(plots[[variant]])) {
         plots[[variant]] <- list(devpars = devpars, which = "TRUE")
     }

biopipen/scripts/regulatory/MotifAffinityTest_MotifBreakR.R

@@ -36,7 +36,7 @@ get_bkg <- function(base) {
 bkg <- c(A = get_bkg("A"), C = get_bkg("C"), G = get_bkg("G"), T = get_bkg("T"))
 
 # run motifbreakR
-log_info("Running motifbreakR ...")
+log$info("Running motifbreakR ...")
 results <- motifbreakR(
     snpList = snps,
     pwmList = mdb,
@@ -48,7 +48,7 @@ results <- motifbreakR(
     BPPARAM = MulticoreParam(ncores)
 )
 
-log_info("Calculating p values ...")
+log$info("Calculating p values ...")
 results <- calculatePvalue(results)
 results_to_save <- as.data.frame(unname(results))
 results_to_save$motifPos <- lapply(results_to_save$motifPos, function(x) paste(x, collapse = ","))
@@ -69,7 +69,7 @@ write.table(
 )
 rm(results_to_save)
 
-log_info("Plotting variants ...")
+log$info("Plotting variants ...")
 if (is.null(plots) || length(plots) == 0) {
     results <- results[order(-abs(results$alleleDiff)), , drop = FALSE]
     results <- results[1:min(plot_nvars, length(results)), , drop = FALSE]
@@ -78,7 +78,7 @@ if (is.null(plots) || length(plots) == 0) {
     variants <- names(plots)
 }
 for (variant in variants) {
-    log_info("- Variant: {variant}")
+    log$info("- Variant: {variant}")
     if (is.null(plots[[variant]])) {
         plots[[variant]] <- list(devpars = devpars, which = "TRUE")
     }

biopipen/scripts/regulatory/VariantMotifPlot.R

@@ -1,8 +1,8 @@
-{{ biopipen_dir | joinpaths: "utils", "misc.R" | source_r }}
-{{ biopipen_dir | joinpaths: "scripts", "regulatory", "motifs-common.R" | source_r }}
+{% include biopipen_dir + "/scripts/regulatory/motifs-common.R" %}
 
 library(BSgenome)
 library(GenomicRanges)
+library(biopipen.utils)
 
 infile <- {{in.infile | r}}
 outdir <- {{out.outdir | r}}
@@ -27,17 +27,19 @@ if (is.null(motif_col) && is.null(regulator_col)) {
     stop("Either motif (envs.motif_col) or regulator (envs.regulator_col) column must be provided")
 }
 
-log_info("Reading input data ...")
+log <- get_logger()
+
+log$info("Reading input data ...")
 indata <- read.table(infile, header=TRUE, sep="\t", stringsAsFactors=FALSE, check.names = FALSE)
 
-log_info("Ensuring regulators in the input data ...")
+log$info("Ensuring regulators in the input data ...")
 indata <- ensure_regulator_motifs(indata, outdir, motif_col, regulator_col, regmotifs, notfound = notfound)
 genome_pkg <- get_genome_pkg(genome)
 
-log_info("Reading motif database ...")
+log$info("Reading motif database ...")
 meme <- read_meme_to_motifdb(motifdb, indata, motif_col, regulator_col, notfound, outdir)
 
-log_info("Composing motifbreakR results from input data ...")
+log$info("Composing motifbreakR results from input data ...")
 indata$chr <- indata$chrom %||% indata$chr %||% indata$seqnames
 indata$seqnames <- NULL
 indata$strand <- indata$strand %||% "+"
@@ -62,7 +64,7 @@ genome(indata) <- genome
 attributes(indata)$genome.package <- genome_pkg
 attributes(indata)$motifs <- meme
 
-log_info("Plotting variants ...")
+log$info("Plotting variants ...")
 if (is.null(plot_vars)) {
     plot_vars <- unique(indata$SNP_id)
 } else if (length(plot_vars) > 1) {
@@ -71,6 +73,6 @@ if (is.null(plot_vars)) {
     plot_vars <- strsplit(plot_vars, ",")[[1]]
 }
 for (pvar in plot_vars) {
-    log_info("- Variant: {pvar}")
+    log$info("- Variant: {pvar}")
     plot_variant_motifs(indata, pvar, devpars, outdir)
 }

biopipen/scripts/regulatory/motifs-common.R

@@ -1,8 +1,7 @@
-# make sure biopipen/utils/misc.R is loaded, log_warn is defined, and slugify is defined
-
 library(rlang)
 library(universalmotif)
 library(MotifDb)
+library(biopipen.utils)
 
 #' @title Common functions for regulatory analysis
 #' @name regulatory-common
@@ -144,11 +143,12 @@ motifdb_to_motiflib <- function(motifdb) {
 #' @param notfound Action to take if regulators are not found in the mapping file
 #' @return Data frame with regulators and motifs
 #' @export
-ensure_regulator_motifs <- function (indata, outdir, motif_col, regulator_col, regmotifs, log_indent = "", notfound = "error") {
+ensure_regulator_motifs <- function (indata, outdir, motif_col, regulator_col, regmotifs, log_indent = "", notfound = "error", log = NULL) {
     if (is.null(motif_col)) {
         if (is.null(regmotifs)) {
             stop("Regulator-motif mapping file (envs.regmotifs) is required when no motif column (envs.motif_col) is provided")
         }
+        log <- log %||% get_logger()
         regmotifs <- .read_regmotifs(regmotifs)
         rm_motif_col <- colnames(regmotifs)[1]
         rm_reg_col <- colnames(regmotifs)[2]
@@ -158,7 +158,7 @@ ensure_regulator_motifs <- function (indata, outdir, motif_col, regulator_col, r
         notfound_regs <- setdiff(regulators, rm_regs)
         .handle_notfound_items(
             notfound_regs,
-            log_warn,
+            log$warn,
             "The following regulators were not found in the regulator-motif mapping file",
             notfound,
             file.path(outdir, "notfound_regulators.txt"),
@@ -185,7 +185,7 @@ ensure_regulator_motifs <- function (indata, outdir, motif_col, regulator_col, r
             notfound_motifs <- setdiff(motifs, rm_motifs)
             .handle_notfound_items(
                 notfound_motifs,
-                log_warn,
+                log$warn,
                 "The following motifs were not found in the regulator-motif mapping file",
                 notfound,
                 file.path(outdir, "notfound_motifs.txt"),
@@ -232,7 +232,8 @@ get_genome_pkg <- function(genome) {
 #' @param outdir Output directory, used to save un-matched motifs
 #' @return Motifs that are found
 #' @export
-check_motifs <- function(motifs, all_motifs, notfound, outdir) {
+check_motifs <- function(motifs, all_motifs, notfound, outdir, log = NULL) {
+    log <- log %||% get_logger()
     notfound_motifs <- setdiff(motifs, all_motifs)
     if (length(notfound_motifs) > 0) {
         first_notfound <- head(notfound_motifs, 3)
@@ -246,15 +247,15 @@ check_motifs <- function(motifs, all_motifs, notfound, outdir) {
             if (notfound == "error") {
                 stop(msg1, "\n", msg2)
             } else if (notfound == "ignore") {
-                log_warn(msg1)
-                log_warn(msg2)
+                log$warn(msg1)
+                log$warn(msg2)
             }
         } else {
             msg <- paste0("The following motifs were not found in the motif database: ", paste(first_notfound, collapse = ", "))
             if (notfound == "error") {
                 stop(msg)
             } else if (notfound == "ignore") {
-                log_warn(msg)
+                log$warn(msg)
             }
         }
 

biopipen/scripts/rnaseq/Simulation-ESCO.R

@@ -2,6 +2,7 @@
 library(ESCO)
 library(rlang)
 library(glue)
+library(biopipen.utils)
 
 args <- {{envs.esco_args | r: todot="-"}}
 args <- args %||% list()
@@ -9,6 +10,8 @@ args <- args %||% list()
 save <- args$save
 args$save <- NULL
 
+log <- get_logger()
+
 if (!is.null(seed)) {
     set.seed(seed)
     args$seed <- seed
@@ -20,12 +23,12 @@ args$verbose <- TRUE
 args$numCores <- ncores
 type <- args$type
 
-log_info("Running simulation ...")
+log$info("Running simulation ...")
 sim <- do_call(escoSimulate, args)
 attributes(sim) <- c(attributes(sim), c(simulation_tool = "ESCO"))
-saveRDS(sim, file.path(outdir, "sim.rds"))
+save_obj(sim, file.path(outdir, "sim.rds"))
 
-log_info("Plotting ...")
+log$info("Plotting ...")
 if (type == "single") {
     asys <- assays(sim)
     datalist = list(`simulated-truth` = asys$TrueCounts)
@@ -36,7 +39,7 @@ if (type == "single") {
         datalist$`down-sampled` = asys$observedcounts
     }
 
-    log_info("- Plotting the data ...")
+    log$info("- Plotting the data ...")
     dataplot <- file.path(outdir, "data.png")
     png(dataplot, width=length(datalist) * 600, height=1200, res=30)
     heatdata(datalist, norm = FALSE, size = 2, ncol = 3)
@@ -44,7 +47,7 @@ if (type == "single") {
 
     rholist <- metadata(sim)$Params@corr
     if (length(rholist) > 0) {
-        log_info("- Plotting the GCN ...")
+        log$info("- Plotting the GCN ...")
         corrgenes <- rownames(rholist[[1]])
         gcnlist = lapply(datalist, function(data)gcn(data, genes = corrgenes))
         gcnlist = append(gcnlist, list("given truth" = rholist[[1]]), 1)
@@ -75,13 +78,13 @@ if (type == "single") {
         datalist$`down-sampled` = asys$observedcounts
     }
 
-    log_info("- Plotting the data ...")
+    log$info("- Plotting the data ...")
     dataplot <- file.path(outdir, "data.png")
     png(dataplot, width=length(datalist) * 600, height=1200, res=30)
     heatdata(datalist, cellinfo = cellinfo, geneinfo = geneinfo, size = 1, ncol = 3)
     dev.off()
 
-    log_info("- Plotting the GCN for all marker genes (i.e. DE genes) across all cell groups ...")
+    log$info("- Plotting the GCN for all marker genes (i.e. DE genes) across all cell groups ...")
     degeneinfo = geneinfo[which(geneinfo$newcelltype!="None"),]
     degeneinfo$newcelltype = droplevels(degeneinfo$newcelltype)
     degcnlist = lapply(datalist, function(data)gcn(data, genes = degeneinfo$genes))
@@ -90,7 +93,7 @@ if (type == "single") {
     heatgcn(degcnlist, geneinfo = degeneinfo, size = 2, ncol = 3)
     dev.off()
 
-    log_info("- Plotting the GCN for marker genes within one cell group ...")
+    log$info("- Plotting the GCN for marker genes within one cell group ...")
     rholist = metadata(sim)$Params@corr
     group2_gcnlist = lapply(datalist,
                             function(data){
@@ -126,7 +129,7 @@ if (type == "single") {
     DEgene.name = as.character(rowData(sim)$Gene[which(group.facs.gene[,1]>1)])
     degeneinfo = geneinfo[match(DEgene.name, geneinfo$genes),]
 
-    log_info("- Plotting the data ...")
+    log$info("- Plotting the data ...")
     dataplot <- file.path(outdir, "data.png")
     png(dataplot, width=2000, height=1200, res=30)
     # plot the data
@@ -151,7 +154,7 @@ if (type == "single") {
     # get the geneinfo
     degenes = which(metadata(sim)$Params@paths.DEgenes==1)
 
-    log_info("- Plotting the trajectory ...")
+    log$info("- Plotting the trajectory ...")
     trajplot <- file.path(outdir, "traj.png")
     png(trajplot, width=1600, height=1200, res=30)
     # plot the data
@@ -160,7 +163,7 @@ if (type == "single") {
             labels = levels(as.factor(colData(sim)$Path)))
     dev.off()
 
-    log_info("- Plotting the data ...")
+    log$info("- Plotting the data ...")
     dataplot <- file.path(outdir, "data.png")
     heatdata(list("simulated truth" = datatrue[degenes,]),
          cellinfo = cellinfo,

biopipen/scripts/rnaseq/Simulation-RUVcorr.R

@@ -1,6 +1,9 @@
 
 library(rlang)
 library(RUVcorr)
+library(biopipen.utils)
+
+log <- get_logger()
 
 args <- {{envs.ruvcorr_args | r: todot="-"}}
 if (!is.null(seed)) { set.seed(seed) }
@@ -17,7 +20,7 @@ args$check <- args$check %||% TRUE
 args$n = ngenes
 args$m = nsamples
 
-log_info("Running simulation ...")
+log$info("Running simulation ...")
 sim <- do_call(simulateGEdata, args)
 attributes(sim) <- c(attributes(sim), c(simulation_tool = "RUVcorr"))
 genes <- paste0("Gene", 1:ngenes)
@@ -35,8 +38,8 @@ sim$Noise <- t(sim$Noise)
 colnames(sim$Sigma) <- genes
 rownames(sim$Sigma) <- genes
 
-log_info("Saving results ...")
-saveRDS(sim, file.path(outdir, "sim.rds"))
-saveRDS(sim$Truth, file.path(outdir, "Truth.rds"))
+log$info("Saving results ...")
+save_obj(sim, file.path(outdir, "sim.rds"))
+save_obj(sim$Truth, file.path(outdir, "Truth.rds"))
 
 simulated <- sim$Y

biopipen/scripts/rnaseq/Simulation.R

@@ -1,5 +1,3 @@
-{{ biopipen_dir | joinpaths: "utils", "misc.R" | source_r }}
-
 ngenes <- {{in.ngenes | r}}
 nsamples <- {{in.nsamples | r}}
 outfile <- {{out.outfile | r}}

biopipen/scripts/rnaseq/UnitConversion.R

@@ -1,7 +1,6 @@
-{{ biopipen_dir | joinpaths: "utils", "misc.R" | source_r }}
-
 library(rlang)
 library(glue)
+library(biopipen.utils)
 
 infile <- {{in.infile | r}}
 outfile <- {{out.outfile | r}}
@@ -11,7 +10,9 @@ refexon <- {{envs.refexon | r}}
 meanfl <- {{envs.meanfl | r}}
 nreads <- {{envs.nreads | r}}
 
-log_info("Reading input data ...")
+log <- get_logger()
+
+log$info("Reading input data ...")
 indata = read.table(infile, header = TRUE, sep = "\t", row.names = 1, check.names = F)
 samples = colnames(indata)
 
@@ -326,7 +327,7 @@ if (grepl('rawcounts|rawcount|counts|count', outunit)) {
     stop(glue("Can't find a supported unit in the outunit: {outunit}\n"))
 }
 
-log_info("Transforming data by resolving {inunit} ...")
+log$info("Transforming data by resolving {inunit} ...")
 if (intype == outtype) {
     fun <- identity
 } else {
@@ -339,5 +340,5 @@ if (intype == outtype) {
 assign(outtype, fun(indata))
 out <- eval(parse_expr(outunit))
 
-log_info("Saving output data ...")
+log$info("Saving output data ...")
 write.table(out, outfile, quote=FALSE, row.names=TRUE, col.names=TRUE, sep="\t")