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

biopipen/scripts/snp/PlinkCallRate.R

@@ -1,7 +1,5 @@
-{{ biopipen_dir | joinpaths: "utils", "misc.R" | source_r }}
-{{ biopipen_dir | joinpaths: "utils", "plot.R" | source_r }}
-library(ggprism)
-theme_set(theme_prism())
+library(plotthis)
+library(biopipen.utils)
 
 indir <- {{in.indir | r}}
 outdir <- {{out.outdir | r}}
@@ -13,11 +11,13 @@ samplecr <- {{envs.samplecr | r}}
 varcr <- {{envs.varcr | r}}
 max_iter <- {{envs.max_iter | r}}
 
+log <- get_logger()
+
 bedfile = Sys.glob(file.path(indir, '*.bed'))
 if (length(bedfile) == 0)
     stop("No bed files found in the input directory.")
 if (length(bedfile) > 1) {
-    log_warn("Multiple bed files found in the input directory. Using the first one.")
+    log$warn("Multiple bed files found in the input directory. Using the first one.")
     bedfile <- bedfile[1]
 }
 input <- tools::file_path_sans_ext(bedfile)
@@ -30,7 +30,7 @@ all_varcr_fail_file = paste0(output, '.varcr.fail')
 if (file.exists(all_smiss_file)) invisible(file.remove(all_smiss_file))
 if (file.exists(all_vmiss_file)) invisible(file.remove(all_vmiss_file))
 for (i in 1:max_iter) {
-    log_info("Iteration {i} ...")
+    log$info("Iteration {i} ...")
     # iter_out <- paste0(output, "-", i)
     iter_dir <- file.path(outdir, paste0("iter", i))
     dir.create(iter_dir, showWarnings = FALSE)
@@ -152,39 +152,48 @@ vmiss <- read.table(
 vmiss$Callrate <- 1 - vmiss$F_MISS
 
 if (doplot) {
-    log_info("Plotting ...")
+    log$info("Plotting ...")
     callrate.sample$Status <- "Pass"
     callrate.sample[callrate.sample.fail, "Status"] <- "Fail"
-    plotGG(
-        data = callrate.sample,
-        geom = "histogram",
-        outfile = paste0(output, '.samplecr.png'),
-        args = list(aes(fill = Status, x = Callrate), alpha = 0.8, bins = 50),
-        ggs = c(
-            'xlab("Sample Call Rate")',
-            'ylab("Count")',
-            'geom_vline(xintercept = samplecr, color = "red", linetype="dashed")',
-            'theme(legend.position = "none")',
-            'geom_text(aes(x = samplecr, y = Inf, label = samplecr), colour="red", angle=90, vjust = 1.2, hjust = 1.2)',
-            'scale_fill_manual(values = c("Pass" = "blue3", "Fail" = "red3"))'
-        )
+    callrate.sample$Status <- factor(callrate.sample$Status, levels = c("Fail", "Pass"))
+
+    p_callrate_file <- paste0(output, '.samplecr.png')
+    p_callrate <- Histogram(
+        callrate.sample,
+        x = "Callrate",
+        group_by = "Status",
+        xlab = "Sample Call Rate",
+        ylab = "Count",
+        palette = "Set1",
+        alpha = 0.8,
+        bins = 50
     )
+    res <- 70
+    height <- attr(p_callrate, "height") * res
+    width <- attr(p_callrate, "width") * res
+    png(p_callrate_file, width = width, height = height, res = res)
+    print(p_callrate)
+    dev.off()
 
     vmiss$Status <- "Pass"
     vmiss[which(vmiss$Callrate < varcr), "Status"] <- "Fail"
-    plotGG(
-        data = vmiss,
-        geom = "histogram",
-        outfile = paste0(output, '.varcr.png'),
-        args = list(aes(fill = Status, x = Callrate), alpha = 0.8, bins = 50),
-        ggs = c(
-            'xlab("Variant Call Rate")',
-            'ylab("Count")',
-            'geom_vline(xintercept = varcr, color = "red", linetype="dashed")',
-            'theme(legend.position = "none")',
-            'geom_text(aes(x = varcr, y = Inf, label = varcr), colour="red", angle=90, vjust = 1.2, hjust = 1.2)',
-            'scale_fill_manual(values = c("Pass" = "blue3", "Fail" = "red3"))'
-        ),
-        devpars = devpars
+    vmiss$Status <- factor(vmiss$Status, levels = c("Fail", "Pass"))
+
+    p_varcr_file <- paste0(output, '.varcr.png')
+    p_varcr <- Histogram(
+        vmiss,
+        x = "Callrate",
+        group_by = "Status",
+        xlab = "Variant Call Rate",
+        ylab = "Count",
+        palette = "Set1",
+        alpha = 0.8,
+        bins = 50
     )
+    res <- 70
+    height <- attr(p_varcr, "height") * res
+    width <- attr(p_varcr, "width") * res
+    png(p_varcr_file, width = width, height = height, res = res)
+    print(p_varcr)
+    dev.off()
 }

biopipen/scripts/snp/PlinkFreq.R

@@ -1,8 +1,6 @@
-{{ biopipen_dir | joinpaths: "utils", "misc.R" | source_r }}
-{{ biopipen_dir | joinpaths: "utils", "plot.R" | source_r }}
 library(rlang)
-library(ggprism)
-theme_set(theme_prism())
+library(plotthis)
+library(biopipen.utils)
 
 indir <- {{in.indir | r}}
 outdir <- {{out.outdir | r}}
@@ -92,7 +90,7 @@ post_process <- function(suffix, snp_col = "ID", sep = "\t", modifier = NULL) {
             lt_flag <- paste0(metric_col, " < ", cutoff)
             freq$GE <- freq[[metric_col]] >= cutoff
             freq$Flag <- ifelse(freq$GE, ge_flag, lt_flag)
-            freq$Flag <- factor(freq$Flag, levels = c(ge_flag, lt_flag))
+            freq$Flag <- factor(freq$Flag, levels = c(lt_flag, ge_flag))
             write.table(
                 freq[[snp_col]][freq$GE],
                 file = paste0(output, suffix, ".", metric_col, ".ge"),
@@ -109,26 +107,22 @@ post_process <- function(suffix, snp_col = "ID", sep = "\t", modifier = NULL) {
             )
 
             if (doplot) {
-                plotGG(
-                    data = freq,
-                    geom = "histogram",
-                    outfile = paste0(output, suffix, ".", metric_col, ".png"),
-                    args = list(aes(x = !!sym(metric_col), fill = Flag), alpha = 0.8, bins = 50),
-                    ggs = c(
-                        sprintf('xlab("%s")', metric_col),
-                        'ylab("Count")',
-                        sprintf('geom_vline(xintercept = %.3f, color = "red", linetype="dashed")', cutoff),
-                        sprintf(
-                            'geom_text(aes(x = %.3f, y = Inf, label = as.character(%.3f)), colour="blue", vjust = 1.5, hjust = -.1)',
-                            cutoff, cutoff
-                        ),
-                        sprintf(
-                            'scale_fill_manual(values = c("%s" = "blue3", "%s" = "green3"))',
-                            ge_flag, lt_flag
-                        )
-                    ),
-                    devpars = devpars
+                p <- Histogram(
+                    freq,
+                    x = metric_col,
+                    group_by = "Flag",
+                    alpha = 0.8,
+                    bins = 50,
+                    xlab = metric_col,
+                    ylab = "Count",
+                    palette = "Set1"
                 )
+                res <- 70
+                height <- attr(p, "height") * res
+                width <- attr(p, "width") * res
+                png(paste0(output, suffix, ".", metric_col, ".png"), width = width, height = height, res = res)
+                print(p)
+                dev.off()
             }
         } else {
             iter_dir <- file.path(outdir, paste0(metric_col, "_filtered"))
@@ -148,6 +142,7 @@ post_process <- function(suffix, snp_col = "ID", sep = "\t", modifier = NULL) {
                 }
             }
             freq$Flag <- ifelse(indicate(freq), "Fail", "Pass")
+            freq$Flag <- factor(freq$Flag, levels = c("Fail", "Pass"))
             failfile <- paste0(output, suffix, ".", metric_col, ".fail")
             write.table(
                 freq[[snp_col]][freq$Flag == "Fail"],
@@ -158,24 +153,22 @@ post_process <- function(suffix, snp_col = "ID", sep = "\t", modifier = NULL) {
             )
 
             if (doplot) {
-                plotGG(
-                    data = freq,
-                    geom = "histogram",
-                    outfile = paste0(output, suffix, ".", metric_col, ".png"),
-                    args = list(aes(x = !!sym(metric_col), fill = Flag), alpha = 0.8, bins = 50),
-                    ggs = c(
-                        sprintf('xlab("%s")', metric_col),
-                        'ylab("Count")',
-                        sprintf('geom_vline(xintercept = %.3f, color = "blue", linetype="dashed")', cutoff),
-                        sprintf(
-                            'geom_text(aes(x = %.3f, y = Inf, label = as.character(%.3f)), colour="blue", vjust = 1.5, hjust = -.1)',
-                            cutoff, cutoff
-                        ),
-                        'theme(legend.position = "none")',
-                        'scale_fill_manual(values = c("Pass" = "blue3", "Fail" = "red3"))'
-                    ),
-                    devpars = devpars
+                p <- Histogram(
+                    freq,
+                    x = metric_col,
+                    group_by = "Flag",
+                    alpha = 0.8,
+                    bins = 50,
+                    xlab = metric_col,
+                    ylab = "Count",
+                    palette = "Set1"
                 )
+                res <- 70
+                height <- attr(p, "height") * res
+                width <- attr(p, "width") * res
+                png(paste0(output, suffix, ".", metric_col, ".png"), width = width, height = height, res = res)
+                print(p)
+                dev.off()
             }
 
             filter_cmd <- c(

biopipen/scripts/snp/PlinkHWE.R

@@ -1,7 +1,5 @@
-{{ biopipen_dir | joinpaths: "utils", "misc.R" | source_r }}
-{{ biopipen_dir | joinpaths: "utils", "plot.R" | source_r }}
-library(ggprism)
-theme_set(theme_prism())
+library(plotthis)
+library(biopipen.utils)
 
 indir <- {{in.indir | r}}
 outdir <- {{out.outdir | r}}
@@ -51,22 +49,29 @@ if (doplot) {
     hardy$Pval <- -log10(hardy$P)
     hardy$Status <- "Pass"
     hardy[which(hardy$SNP %in% hardy.fail$SNP), "Status"] <- "Fail"
+    hardy$Status <- factor(hardy$Status, levels = c("Fail", "Pass"))
 
-    plotGG(
-        data = hardy,
-        geom = "histogram",
-        outfile = paste0(output, '.hardy.png'),
-        args = list(aes(x = Pval, fill = Status), alpha = 0.8, bins = 50),
-        ggs = c(
-            'xlab("-log10(HWE p-value)")',
-            'ylab("Count")',
-            'geom_vline(xintercept = -log10(cutoff), color = "red", linetype="dashed")',
-            'theme(legend.position = "none")',
-            'geom_text(aes(x = -log10(cutoff), y = Inf, label = cutoff), colour="red", angle=90, vjust = 1.2, hjust = 1.2)',
-            'scale_fill_manual(values = c("Pass" = "blue3", "Fail" = "red3"))'  # Added line to set "Fail" color to red
-        ),
-        devpars = devpars
+    p <- Histogram(
+        hardy,
+        x = "Pval",
+        group_by = "Status",
+        alpha = 0.8,
+        bins = 50,
+        xlab = "-log10(HWE p-value)",
+        ylab = "Count",
+        palette = "Set1"
     )
+    res <- 70
+    height <- attr(p, "height") * res
+    width <- attr(p, "width") * res
+    png(
+        filename = paste0(output, '.hardy.png'),
+        width = width,
+        height = height,
+        res = res
+    )
+    print(p)
+    dev.off()
 }
 
 cmd <- c(

biopipen/scripts/snp/PlinkHet.R

@@ -1,7 +1,5 @@
-{{ biopipen_dir | joinpaths: "utils", "misc.R" | source_r }}
-{{ biopipen_dir | joinpaths: "utils", "plot.R" | source_r }}
-library(ggprism)
-theme_set(theme_prism())
+library(plotthis)
+library(biopipen.utils)
 
 indir <- {{in.indir | r}}
 outdir <- {{out.outdir | r}}
@@ -11,11 +9,13 @@ cutoff <- {{envs.cutoff | r}}
 doplot <- {{envs.plot | r}}
 devpars <- {{envs.devpars | r}}
 
+log <- get_logger()
+
 bedfile = Sys.glob(file.path(indir, '*.bed'))
 if (length(bedfile) == 0)
     stop("No bed files found in the input directory.")
 if (length(bedfile) > 1) {
-    log_warn("Multiple bed files found in the input directory. Using the first one.")
+    log$warn("Multiple bed files found in the input directory. Using the first one.")
     bedfile <- bedfile[1]
 }
 input <- tools::file_path_sans_ext(bedfile)
@@ -60,25 +60,29 @@ writeLines(het.fail, con = file(paste0(output, '.het.fail')))
 if (doplot) {
     het$Status <- "Pass"
     het[het.fail, "Status"] <- "Fail"
+    het$Status <- factor(het$Status, levels = c("Fail", "Pass"))
 
-    plotGG(
-        data = het,
-        geom = "histogram",
-        outfile = paste0(output, '.het.png'),
-        args = list(aes(fill = Status, x = Het), alpha = 0.8, bins = 50),
-        ggs = c(
-            'xlab("Sample Heterozygosity")',
-            'ylab("Count")',
-            'geom_vline(xintercept = c(het.mean-cutoff*het.sd, het.mean+cutoff*het.sd), color = "red", linetype="dashed")',
-            'geom_vline(xintercept = het.mean, color = "blue", linetype="dashed")',
-            'theme(legend.position = "none")',
-            'geom_text(aes(x = het.mean-cutoff*het.sd, y = Inf, label = sprintf("mean - %ssd (%.3f)", cutoff, het.mean - cutoff*het.sd)), colour="red", angle=90, vjust = 1.2, hjust = 1.2)',
-            'geom_text(aes(x = het.mean+cutoff*het.sd, y = Inf, label = sprintf("mean + %ssd (%.3f)", cutoff, het.mean + cutoff*het.sd)), colour="red", angle=90, vjust = 1.2, hjust = 1.2)',
-            'geom_text(aes(x = het.mean, y = Inf, label = sprintf("mean (%.3f)", het.mean)), colour="blue", vjust = 1.5, hjust = -.1)',
-            'scale_fill_manual(values = c("Pass" = "blue3", "Fail" = "red3"))'
-        ),
-        devpars = devpars
+    p <- Histogram(
+        het,
+        x = "Het",
+        group_by = "Status",
+        alpha = 0.8,
+        bins = 50,
+        xlab = "Sample Heterozygosity",
+        ylab = "Count",
+        palette = "Set1"
+    )
+    res <- 70
+    height <- attr(p, "height") * res
+    width <- attr(p, "width") * res
+    png(
+        filename = paste0(output, '.het.png'),
+        width = width,
+        height = height,
+        res = res
     )
+    print(p)
+    dev.off()
 }
 
 cmd <- c(

biopipen/scripts/snp/PlinkIBD.R

@@ -1,9 +1,9 @@
-{{ biopipen_dir | joinpaths: "utils", "misc.R" | source_r }}
-{{ biopipen_dir | joinpaths: "utils", "plot.R" | source_r }}
 suppressPackageStartupMessages({
     library(dplyr)
     library(tidyr)
     library(tibble)
+	library(plotthis)
+	library(biopipen.utils)
 })
 
 indir    <- {{in.indir | r}}
@@ -19,11 +19,13 @@ doplot   <- {{envs.plot | r}}
 seed     <- {{envs.seed | r}}
 ncores   <- {{envs.ncores | r}}
 
+log <- get_logger()
+
 bedfile <- Sys.glob(file.path(indir, '*.bed'))
 if (length(bedfile) == 0)
     stop("No bed files found in the input directory.")
 if (length(bedfile) > 1) {
-    log_warn("Multiple bed files found in the input directory. Using the first one.")
+    log$warn("Multiple bed files found in the input directory. Using the first one.")
     bedfile <- bedfile[1]
 }
 input  <- tools::file_path_sans_ext(bedfile)
@@ -153,48 +155,42 @@ if (doplot) {
 	rownames(similarity) <- samids
 	colnames(similarity) <- samids
 
-	annos <- list()
+	andata <- NULL
+	column_annotation <- NULL
 	if (!is.null(annofile) && !isFALSE(annofile)) {
 		options(stringsAsFactors = TRUE)
 		andata <- read.table(annofile, header = TRUE, row.names = 1, sep = "\t", check.names = FALSE)
 		andata <- andata[samids, , drop = FALSE]
 		for (anname in colnames(andata)) {
-			annos[[anname]] <- as.matrix(andata[, anname])
+			column_annotation <- c(column_annotation, anname)
 		}
-		annos$annotation_name_gp <- fontsize8
-		annos <- do.call(HeatmapAnnotation, annos)
 	}
 
-	args <- list(
+	p <- plotthis::Heatmap(
+		similarity,
 		name = "PI_HAT",
-		cell_fun = function(j, i, x, y, width, height, fill) {
-			if (similarity[i, j] > pihat && i != j)
-				grid.points(x, y, pch = 4, size = unit(.5, "char"))
-		},
-		#heatmap_legend_param = list(
-		#	title_gp  = fontsize9,
-		#	labels_gp = fontsize8
-		#),
+        in_form = "matrix",
+        cell_type = "label",
+		rows_data = andata,
+		label = function(x) ifelse (x > pihat, '*', NA),
+        title = paste0("(*) PI_HAT > ", pihat),
 		clustering_distance_rows = function(m) as.dist(1-m),
 		clustering_distance_columns = function(m) as.dist(1-m),
-		top_annotation = if (length(annos) == 0) NULL else annos
+        show_row_names = TRUE,
+        show_column_names = TRUE,
+		column_annotation = column_annotation
 	)
 
-	plotHeatmap(
-		similarity,
-		outfile = paste0(output, '.ibd.png'),
-		args = args,
-		draw = list(
-			annotation_legend_list = list(
-				Legend(
-					labels = paste(">", pihat),
-					title = "",
-					type = "points",
-					pch = 4,
-					title_gp = fontsize9,
-					labels_gp = fontsize8)),
-			merge_legend = TRUE
-        ),
-		devpars = devpars
-    )
+	res <- 100
+	height <- attr(p, "height") * res
+	width <- attr(p, "width") * res
+	png(
+		filename = paste0(output, '.ibd.png'),
+		width = width,
+		height = height,
+		res = res
+	)
+	print(p)
+	dev.off()
+
 }

biopipen/scripts/stats/ChowTest.R

@@ -1,7 +1,6 @@
-{{ biopipen_dir | joinpaths: "utils", "misc.R" | source_r }}
-
 library(rlang)
 library(dplyr)
+library(biopipen.utils)
 
 infile <- {{in.infile | r}}
 groupfile <- {{in.groupfile | r}}
@@ -11,7 +10,9 @@ padj <- {{envs.padj | r}}
 transpose_input <- {{envs.transpose_input | r}}
 transpose_group <- {{envs.transpose_group | r}}
 
-log_info("Reading input files ...")
+log <- get_logger()
+
+log$info("Reading input files ...")
 indata <- read.table(infile, header = TRUE, sep = "\t", row.names = 1, check.names = FALSE)
 if (transpose_input) {
 	indata <- t(indata)
@@ -105,16 +106,16 @@ formatlm <- function(m, g = NULL, type = "coeff") {
 	}
 }
 
-log_info("Running Chow tests ...")
+log$info("Running Chow tests ...")
 ncases <- nrow(fmldata)
 results <- do_call(rbind, lapply(
     seq_len(ncases),
     function(i) {
 		fmlrow <- fmldata[i, , drop=TRUE]
         if (i %% 100 == 0) {
-            log_info("- {i} / {ncases} ...")
+            log$info("- {i} / {ncases} ...")
         }
-        log_debug("  Running Chow test for formula: {fmlrow$Formula} (grouping = {fmlrow$Group})")
+        log$debug("  Running Chow test for formula: {fmlrow$Formula} (grouping = {fmlrow$Group})")
 
         res <- chow.test(fmlrow$Formula, fmlrow$Group)
 		fmlrow$Pooled_Coef <- formatlm(res$pooled.lm)
@@ -135,11 +136,11 @@ results <- do_call(rbind, lapply(
 )) %>% as.data.frame()
 
 if (padj != "none") {
-    log_info("Adjusting p-values ...")
+    log$info("Adjusting p-values ...")
     results$Padj <- p.adjust(results$Pval, method = padj)
 }
 
-log_info("Writing output ...")
+log$info("Writing output ...")
 # unimplemented type 'list' in 'EncodeElement'
 results <- apply(results, 2, as.character)
 write.table(results, file = outfile, sep = "\t", quote = FALSE, row.names = FALSE)

biopipen/scripts/stats/DiffCoexpr.R

@@ -1,4 +1,3 @@
-{{ biopipen_dir | joinpaths: "utils", "misc.R" | source_r }}
 library(dcanr)
 library(scuttle)
 library(doRNG)
@@ -6,6 +5,7 @@ library(doParallel)
 library(snpStats)
 library(rlang)
 library(dplyr)
+library(biopipen.utils)
 
 infile <- {{in.infile | r}}
 groupfile <- {{in.groupfile | r}}
@@ -19,12 +19,14 @@ ncores <- {{envs.ncores | r}}
 transpose_input <- {{envs.transpose_input | r}}
 transpose_group <- {{envs.transpose_group | r}}
 
-log_info("Setting seed and parallel backend ...")
+log <- get_logger()
+
+log$info("Setting seed and parallel backend ...")
 set.seed(seed)
 registerDoParallel(cores = ncores)
 registerDoRNG(seed)
 
-log_info("Reading input files ...")
+log$info("Reading input files ...")
 indata <- read.table(infile, header = TRUE, row.names = 1, sep = "\t", check.names = FALSE)
 if (transpose_input) {
     indata <- t(indata)
@@ -42,21 +44,21 @@ diffcoex_score <- function(group) {
 
     gvals <- unique(gdata[, group, drop = TRUE])
     if (length(gvals) < 2) {
-        log_debug("  Less than 2 groups in the input. Skipping ...")
+        log$debug("  Less than 2 groups in the input. Skipping ...")
         return(NULL)
     }
     rs <- lapply(gvals, function(gval) {
         samples <- rownames(gdata[gdata[[group]] == gval, , drop = FALSE])
         expr <- indata[samples, , drop = FALSE]
         if (length(samples) < 3) {
-            log_debug("  Less than 3 samples in one of the groups. Skipping ...")
+            log$debug("  Less than 3 samples in one of the groups. Skipping ...")
             return(NULL)
         }
         cor.pairs(as.matrix(expr), cor.method = method)
     })
     rs[sapply(rs, is.null)] <- NULL
     if (length(rs) < 2) {
-        log_debug("  Less than 2 groups with at least 3 samples. Skipping ...")
+        log$debug("  Less than 2 groups with at least 3 samples. Skipping ...")
         return(NULL)
     }
     N <- length(rs)
@@ -130,21 +132,21 @@ perm_test <- function(dcscores, group, B = perm_batch) {
 
 do_one_group <- function(i) {
     group <- colnames(gdata)[i]
-    log_info("- Processing group {i}/{ngroups}: {group} ...")
-    log_info("  Calculating differential co-expression scores ...")
+    log$info("- Processing group {i}/{ngroups}: {group} ...")
+    log$info("  Calculating differential co-expression scores ...")
     dcscores <- diffcoex_score(group)
 
     if (!is.null(dcscores)) {
-        log_info("  Calculating p-values ...")
+        log$info("  Calculating p-values ...")
         perm_test(dcscores, group)
     }
 }
 
 trios <- do_call(rbind, lapply(seq_len(ngroups), do_one_group))
 if (padj != "none") {
-    log_info("Correcting p-values ...")
+    log$info("Correcting p-values ...")
     trios$Padj <- p.adjust(trios$Pval, method = padj)
 }
 
-log_info("Writing output ...")
+log$info("Writing output ...")
 write.table(trios, file = outfile, sep = "\t", quote = FALSE, row.names = FALSE)

biopipen/scripts/stats/LiquidAssoc.R

@@ -1,12 +1,11 @@
-{{ biopipen_dir | joinpaths: "utils", "misc.R" | source_r }}
-
 library(rlang)
 library(dplyr)
 library(tidyr)
 library(fastLiquidAssociation)
+library(biopipen.utils)
 
 infile <- {{in.infile | r}}
-covfile <- {{in.covfile | r}}
+covfile <- {{in.covfile | r: quote_none=False | r}}
 groupfile <- {{in.groupfile | r}}
 fmlfile <- {{in.fmlfile | r}}
 outfile <- {{out.outfile | r}}
@@ -32,7 +31,7 @@ if (!is.null(groupfile) && !is.null(nvec)) {
 	stop("Must provide either in.groupfile or envs.nvec, not both")
 }
 
-log_info("Reading and preparing data ...")
+log$info("Reading and preparing data ...")
 indata <- read.table(infile, header = TRUE, sep = "\t", row.names = 1, check.names = FALSE)
 if (transpose_input) {
 	indata <- t(indata)
@@ -76,7 +75,7 @@ if (!is.null(groupfile)) {
 	nvec <- expand_range(nvec)
 }
 
-log_info("Running fastLiquidAssociation ...")
+log$info("Running fastLiquidAssociation ...")
 indata <- as.matrix(indata)
 mla <- fastMLA(
 	data = indata,
@@ -88,7 +87,7 @@ mla <- fastMLA(
 )
 
 if (nrow(mla) == 0) {
-	log_warn("No significant associations found")
+	log$warn("No significant associations found")
 	out <- data.frame(
 		X12 = character(),
 		X21 = character(),
@@ -128,9 +127,9 @@ if (!is.null(xyz_names)) {
 }
 
 if (padj != "none") {
-	log_info("Calculating adjusted p-values ...")
+	log$info("Calculating adjusted p-values ...")
 	out$Padj <- p.adjust(out$Pval, method = padj)
 }
 
-log_info("Writing output ...")
+log$info("Writing output ...")
 write.table(out, file = outfile, sep = "\t", quote = FALSE, row.names = FALSE)