# HG changeset patch # User bgruening # Date 1631476128 0 # Node ID 224721e768691d7b75d5350602f122f41c90931d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 08c6fd3885bdfbf8b5c3f4dcc2d04729b577e3e1" diff -r 000000000000 -r 224721e76869 macros.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macros.xml Sun Sep 12 19:48:48 2021 +0000 @@ -0,0 +1,30 @@ + + 0 + + 0.1.1 + + + music-deconvolution + r-cowplot + r-reshape2 + + + + ^(([A-Za-z0-9+_ -]+)\s?,?)*$ + + + ^(([A-Za-z0-9+_ -]+)\s?)*$ + + + + + + + + ^(([A-Za-z0-9+_ -@.:/]+)\s?)*$ + + + diff -r 000000000000 -r 224721e76869 music-deconvolution.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/music-deconvolution.xml Sun Sep 12 19:48:48 2021 +0000 @@ -0,0 +1,246 @@ + + estimate cell type proportions in bulk RNA-seq data + + macros.xml + + + + + + +null_str_vec = function(gstr){ + tokens = unlist(as.vector(strsplit(gstr, split=","))) + if (length(tokens) == 0){ + return(NULL) + } + if (length(tokens) == 1){ + return(tokens[[1]]) + } + return(tokens) +} + +bulk_eset = readRDS('$bulk_eset') +scrna_eset = readRDS('$scrna_eset') + +#if str($do.method) == "estimateprops": + +phenotype_factors = null_str_vec('$do.phenotype_factors') +celltypes_label = null_str_vec('$do.celltypes_label') +samples_label = null_str_vec('$do.samples_label') +celltypes = null_str_vec('$do.celltypes') +methods = null_str_vec('$do.methods') +phenotype_gene = null_str_vec('$do.phenotype_gene') +sample_groups = null_str_vec('$do.sample_groups') +sample_disease_group = null_str_vec('$do.sample_disease_group') +sample_disease_group_scale = as.integer('$do.sample_disease_group_scale') +healthy_phenotype = null_str_vec('$do.healthy_phenotype') +compare_title = null_str_vec('$do.compare_title') +outfile_pdf='$out_pdf' + +#elif str($do.method) == "dendrogram": + +celltypes_label = null_str_vec('$do.celltypes_label') +clustertype_label = null_str_vec('$do.clustertype_label') +samples_label = null_str_vec('$do.samples_label') +celltypes = null_str_vec('$do.celltypes') + +data.to.use = list( + #for $i, $repeat in enumerate( $do.cluster_groups ) + #if $i == 0: + $repeat.cluster_id = list(cell.types = null_str_vec('$repeat.celltypes'), + marker.names = null_str_vec('$repeat.marker_name'), + marker.list = read_list('$repeat.marker_list')) + #else + , $repeat.cluster_id = list(cell.types = null_str_vec('$repeat.celltypes'), + marker.names = null_str_vec('$repeat.marker_name'), + marker.list = read_list('$repeat.marker_list')) + #end if + #end for +) + +outfile_pdf='$out_pdf' +outfile_tab='$out_tab' + +#else + stop("No such option") +#end if + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + do["method"] == "dendrogram" + + + do["method"] == "estimateprops" + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + https://doi.org/10.1038/s41467-018-08023-x + + \ No newline at end of file diff -r 000000000000 -r 224721e76869 scripts/dendrogram.R --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/scripts/dendrogram.R Sun Sep 12 19:48:48 2021 +0000 @@ -0,0 +1,83 @@ +## +suppressWarnings(suppressPackageStartupMessages(library(xbioc))) +suppressWarnings(suppressPackageStartupMessages(library(MuSiC))) +suppressWarnings(suppressPackageStartupMessages(library(reshape2))) +suppressWarnings(suppressPackageStartupMessages(library(cowplot))) +## We use this script to generate a clustering dendrogram of cell +## types, using the prior labelling from scRNA. + +read_list <- function(lfile) { + if (lfile == "None") { + return(NULL) + } + return(read.table(file = lfile, header = FALSE, + stringsAsFactors = FALSE)$V1) +} + +args <- commandArgs(trailingOnly = TRUE) +source(args[1]) + +## We then perform bulk tissue cell type estimation with pre-grouping +## of cell types: C, list_of_cell_types, marker genes name, marker +## genes list. +## data.to.use = list( +## "C1" = list(cell.types = c("Neutro"), +## marker.names=NULL, +## marker.list=NULL), +## "C2" = list(cell.types = c("Podo"), +## marker.names=NULL, +## marker.list=NULL), +## "C3" = list(cell.types = c("Endo","CD-PC","LOH","CD-IC","DCT","PT"), +## marker.names = "Epithelial", +## marker.list = read_list("../test-data/epith.markers")), +## "C4" = list(cell.types = c("Macro","Fib","B lymph","NK","T lymph"), +## marker.names = "Immune", +## marker.list = read_list("../test-data/immune.markers")) +## ) +grouped_celltypes <- lapply(data.to.use, function(x) { + x$cell.types +}) +marker_groups <- lapply(data.to.use, function(x) { + x$marker.list +}) +names(marker_groups) <- names(data.to.use) + + +## Perform the estimation +## Produce the first step information +sub.basis <- music_basis(scrna_eset, clusters = celltypes_label, + samples = samples_label, + select.ct = celltypes) + +## Plot the dendrogram of design matrix and cross-subject mean of +## realtive abundance +par(mfrow = c(1, 2)) +d <- dist(t(log(sub.basis$Disgn.mtx + 1e-6)), method = "euclidean") +## Hierarchical clustering using Complete Linkage +hc1 <- hclust(d, method = "complete") +## Plot the obtained dendrogram +plot(hc1, cex = 0.6, hang = -1, main = "Cluster log(Design Matrix)") +d <- dist(t(log(sub.basis$M.theta + 1e-8)), method = "euclidean") +## Hierarchical clustering using Complete Linkage +hc2 <- hclust(d, method = "complete") +## Plot the obtained dendrogram +pdf(file = outfile_pdf, width = 8, height = 8) +plot(hc2, cex = 0.6, hang = -1, main = "Cluster log(Mean of RA)") + +cl_type <- as.character(scrna_eset[[celltypes_label]]) + +for (cl in seq_len(length(grouped_celltypes))) { + cl_type[cl_type %in% grouped_celltypes[[cl]]] <- names(grouped_celltypes)[cl] +} +pData(scrna_eset)[[clustertype_label]] <- factor( + cl_type, levels = c(names(grouped_celltypes), + "CD-Trans", "Novel1", "Novel2")) + +est_bulk <- music_prop.cluster( + bulk.eset = bulk_eset, sc.eset = scrna_eset, + group.markers = marker_groups, clusters = celltypes_label, + groups = clustertype_label, samples = samples_label, + clusters.type = grouped_celltypes) + +write.table(est_bulk, file = outfile_tab, quote = F, col.names = NA, sep = "\t") +dev.off() diff -r 000000000000 -r 224721e76869 scripts/estimateprops.R --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/scripts/estimateprops.R Sun Sep 12 19:48:48 2021 +0000 @@ -0,0 +1,93 @@ +suppressWarnings(suppressPackageStartupMessages(library(xbioc))) +suppressWarnings(suppressPackageStartupMessages(library(MuSiC))) +suppressWarnings(suppressPackageStartupMessages(library(reshape2))) +suppressWarnings(suppressPackageStartupMessages(library(cowplot))) +## We use this script to estimate the effectiveness of proportion methods + +## Load Conf +args <- commandArgs(trailingOnly = TRUE) +source(args[1]) + +## Estimate cell type proportions +est_prop <- music_prop( + bulk.eset = bulk_eset, sc.eset = scrna_eset, + clusters = celltypes_label, + samples = samples_label, select.ct = celltypes, verbose = T) + + +## Show different in estimation methods +## Jitter plot of estimated cell type proportions +jitter.fig <- Jitter_Est( + list(data.matrix(est_prop$Est.prop.weighted), + data.matrix(est_prop$Est.prop.allgene)), + method.name = methods, title = "Jitter plot of Est Proportions") + + +## Make a Plot +## A more sophisticated jitter plot is provided as below. We separated +## the T2D subjects and normal subjects by their HbA1c levels. +m_prop <- rbind(melt(est_prop$Est.prop.weighted), + melt(est_prop$Est.prop.allgene)) + +colnames(m_prop) <- c("Sub", "CellType", "Prop") + +m_prop$CellType <- factor(m_prop$CellType, levels = celltypes) # nolint +m_prop$Method <- factor(rep(methods, each = 89 * 6), levels = methods) # nolint +m_prop$HbA1c <- rep(bulk_eset$hba1c, 2 * 6) # nolint +m_prop <- m_prop[!is.na(m_prop$HbA1c), ] +m_prop$Disease <- factor(sample_groups[(m_prop$HbA1c > 6.5) + 1], # nolint + levels = sample_groups) + +m_prop$D <- (m_prop$Disease == # nolint + sample_disease_group) / sample_disease_group_scale +m_prop <- rbind(subset(m_prop, Disease == healthy_phenotype), + subset(m_prop, Disease != healthy_phenotype)) + +jitter.new <- ggplot(m_prop, aes(Method, Prop)) + + geom_point(aes(fill = Method, color = Disease, stroke = D, shape = Disease), + size = 2, alpha = 0.7, + position = position_jitter(width = 0.25, height = 0)) + + facet_wrap(~ CellType, scales = "free") + + scale_colour_manual(values = c("white", "gray20")) + + scale_shape_manual(values = c(21, 24)) + theme_minimal() + +## Plot to compare method effectiveness +## Create dataframe for beta cell proportions and HbA1c levels +m_prop_ana <- data.frame(pData(bulk_eset)[rep(1:89, 2), phenotype_factors], + ct.prop = c(est_prop$Est.prop.weighted[, 2], + est_prop$Est.prop.allgene[, 2]), + Method = factor(rep(methods, each = 89), + levels = methods)) +colnames(m_prop_ana)[1:4] <- phenotype_factors +m_prop_ana <- subset(m_prop_ana, !is.na(m_prop_ana[phenotype_gene])) +m_prop_ana$Disease <- factor(sample_groups[( # nolint + m_prop_ana[phenotype_gene] > 6.5) + 1], sample_groups) +m_prop_ana$D <- (m_prop_ana$Disease == # nolint + sample_disease_group) / sample_disease_group_scale + +jitt_compare <- ggplot(m_prop_ana, aes_string(phenotype_gene, "ct.prop")) + + geom_smooth(method = "lm", se = FALSE, col = "black", lwd = 0.25) + + geom_point(aes(fill = Method, color = Disease, stroke = D, shape = Disease), + size = 2, alpha = 0.7) + facet_wrap(~ Method) + + ggtitle(compare_title) + theme_minimal() + + scale_colour_manual(values = c("white", "gray20")) + + scale_shape_manual(values = c(21, 24)) + + +pdf(file = outfile_pdf, width = 8, height = 8) +plot_grid(jitter.fig, jitter.new, labels = "auto", ncol = 1, nrow = 2) +jitt_compare +dev.off() + +## Summary table +for (meth in methods) { + ##lm_beta_meth = lm(ct.prop ~ age + bmi + hba1c + gender, data = + ##subset(m_prop_ana, Method == meth)) + lm_beta_meth <- lm(as.formula( + paste("ct.prop", paste(phenotype_factors, collapse = " + "), + sep = " ~ ")), + data = subset(m_prop_ana, Method == meth)) + print(paste0("Summary: ", meth)) + capture.output(summary(lm_beta_meth), + file = paste0("report_data/summ_", meth, ".txt")) +} diff -r 000000000000 -r 224721e76869 scripts/inspect.R --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/scripts/inspect.R Sun Sep 12 19:48:48 2021 +0000 @@ -0,0 +1,25 @@ + +suppressWarnings(suppressPackageStartupMessages(library(xbioc))) +suppressWarnings(suppressPackageStartupMessages(library(MuSiC))) + +args <- commandArgs(trailingOnly = TRUE) +source(args[1]) + +printout <- function(text) { + if (typeof(text) %in% c("list", "vector")) { + write.table(text, file = outfile_tab, quote = F, sep = "\t", + col.names = NA) + } else { + ## text + capture.output(text, file = outfile_tab) # nolint + } +} + +if (inspector %in% c("print", "pData", "fData", "dims", "experimentData", + "exprs", "signature", "annotation", "abstract")) { + op <- get(inspector) + tab <- op(rds_eset) + printout(tab) +} else { + stop(paste0("No such option:", inspector)) +} diff -r 000000000000 -r 224721e76869 test-data/EMTABesethealthy.subset.rds Binary file test-data/EMTABesethealthy.subset.rds has changed diff -r 000000000000 -r 224721e76869 test-data/GSE50244bulkeset.subset.rds Binary file test-data/GSE50244bulkeset.subset.rds has changed diff -r 000000000000 -r 224721e76869 test-data/Mousebulkeset.rds Binary file test-data/Mousebulkeset.rds has changed diff -r 000000000000 -r 224721e76869 test-data/Mousesubeset.degenesonly2.half.rds Binary file test-data/Mousesubeset.degenesonly2.half.rds has changed diff -r 000000000000 -r 224721e76869 test-data/array.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/array.tsv Sun Sep 12 19:48:48 2021 +0000 @@ -0,0 +1,4 @@ + Sample1 Sample2 +Gene1 1 3 +Gene2 2 4 +Gene3 3 5 diff -r 000000000000 -r 224721e76869 test-data/default_output.pdf Binary file test-data/default_output.pdf has changed diff -r 000000000000 -r 224721e76869 test-data/dendro.pdf Binary file test-data/dendro.pdf has changed diff -r 000000000000 -r 224721e76869 test-data/epith.markers --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/epith.markers Sun Sep 12 19:48:48 2021 +0000 @@ -0,0 +1,2614 @@ +Rp1 +Sox17 +1700034P13Rik +Prex2 +Sulf1 +Xkr9 +Eya1 +Sbspon +D030040B21Rik +Crispld1 +Il17f +Mcm3 +Kcnq5 +Col19a1 +Khdrbs2 +Bend6 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+0000 +++ b/test-data/pheno.tsv Sun Sep 12 19:48:48 2021 +0000 @@ -0,0 +1,3 @@ + gender type score +Sample1 1 3 5 +Sample2 2 4 9