# HG changeset patch
# User bgruening
# Date 1631476152 0
# Node ID 2cfd0db49bbcfe05ff715dfe8890c31dc370f2d7
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 08c6fd3885bdfbf8b5c3f4dcc2d04729b577e3e1"
diff -r 000000000000 -r 2cfd0db49bbc construct_eset.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/construct_eset.xml Sun Sep 12 19:49:12 2021 +0000
@@ -0,0 +1,211 @@
+
+ Create an ExpressionSet object from tabular and textual data
+
+ macros.xml
+
+
+
+
+
+
+suppressWarnings(suppressPackageStartupMessages(library(xbioc)))
+suppressWarnings(suppressPackageStartupMessages(library(MuSiC)))
+
+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)
+}
+
+## Assay Data
+## F rows of features and S columns of samples
+## - This file is the only non-optional parameter
+exprs_file = '$exprs_file'
+exprs = as.matrix(read.table(exprs_file, header = T, sep = "\t",
+ row.names = 1, as.is = T))
+## Phenotype Data
+## S rows of samples, and V columns of covariates (e.g. sex, age, etc.)
+pdata = NULL
+#if '$pdata_file':
+pdata_file = '$pdata_file'
+pdata = read.table(pdata_file, row.names = 1, header = T, sep = "\t", as.is=T)
+#end if
+## Annotation and Feature Data, or just a string for type of chip used
+annotation = null_str_vec('$annotation')
+
+if (all(rownames(pdata) != colnames(exprs))) {
+ stop("Number of Samples between phenotypes and assays are not the same")
+}
+
+##metadata = data.frame(
+## labelDescription = c(
+## "Patient gender",
+## "Case/Control",
+## "Tumor progress"),
+## row.names = c("gender", "type", "score"))
+metadata = as.data.frame(do.call(rbind, list(
+#for i, row in enumerate($metadata):
+ #if i==0
+ list(ldesc='$row.label_desc', lname='$row.row_names')
+ #else
+ ,list(ldesc='$row.label_desc', lname='$row.row_names')
+ #end if
+#end for
+)))
+metadata\$labelDescription = unlist(metadata\$ldesc)
+rownames(metadata) = unlist(metadata\$lname)
+metadata\$ldesc = NULL
+metadata\$lname = NULL
+
+if (nrow(metadata)==0) {
+ metadata = NULL
+}
+
+pheno_data = new("AnnotatedDataFrame", data = pdata, varMetadata = metadata)
+
+## Experiment Description -- using the MIAME object
+experiment_data = new(
+ "MIAME",
+ name = null_str_vec('$expdata.name'),
+ lab = null_str_vec('$expdata.lab'),
+ contact = null_str_vec('$expdata.contact'),
+ title = null_str_vec('$expdata.title'),
+ abstract = null_str_vec('$expdata.abstract'),
+ url = null_str_vec('$expdata.url'),
+ other = list(
+#for i, row in enumerate($expdata.other):
+ #if i==0
+ '$row.field' = null_str_vec('$row.comment')
+ #else
+ ,'$row.field' = null_str_vec('$row.comment')
+ #end if
+#end for
+))
+
+e_set = ExpressionSet(assayData = exprs,
+ phenoData = pheno_data,
+ experimentData = experiment_data,
+ annotation = annotation)
+
+capture.output(print(e_set), file = '$out_tab')
+saveRDS(e_set, file= '$out_rds')
+
+
+
+
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+
+
+
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+
+
+ `_ and the `rdocumentation `_
+.
+ ]]>
+
+
+ @misc{falcon2007introduction,
+ title={An introduction to bioconductor’s expressionset class},
+ author={Falcon, Seth and Morgan, Martin and Gentleman, Robert},
+ year={2007}
+ }
+
+
+
\ No newline at end of file
diff -r 000000000000 -r 2cfd0db49bbc macros.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/macros.xml Sun Sep 12 19:49:12 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 2cfd0db49bbc scripts/dendrogram.R
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/scripts/dendrogram.R Sun Sep 12 19:49:12 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$M.theta + 1e-8)), method = "euclidean")
+## Hierarchical clustering using Complete Linkage
+hc2 <- hclust(d, method = "complete")
+## Plot the obtained dendrogram
+pdf(file = outfile_pdf, width = 8, height = 8)
+plot(hc2, cex = 0.6, hang = -1, main = "Cluster log(Mean of RA)")
+
+cl_type <- as.character(scrna_eset[[celltypes_label]])
+
+for (cl in seq_len(length(grouped_celltypes))) {
+ cl_type[cl_type %in% grouped_celltypes[[cl]]] <- names(grouped_celltypes)[cl]
+}
+pData(scrna_eset)[[clustertype_label]] <- factor(
+ cl_type, levels = c(names(grouped_celltypes),
+ "CD-Trans", "Novel1", "Novel2"))
+
+est_bulk <- music_prop.cluster(
+ bulk.eset = bulk_eset, sc.eset = scrna_eset,
+ group.markers = marker_groups, clusters = celltypes_label,
+ groups = clustertype_label, samples = samples_label,
+ clusters.type = grouped_celltypes)
+
+write.table(est_bulk, file = outfile_tab, quote = F, col.names = NA, sep = "\t")
+dev.off()
diff -r 000000000000 -r 2cfd0db49bbc scripts/estimateprops.R
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/scripts/estimateprops.R Sun Sep 12 19:49:12 2021 +0000
@@ -0,0 +1,93 @@
+suppressWarnings(suppressPackageStartupMessages(library(xbioc)))
+suppressWarnings(suppressPackageStartupMessages(library(MuSiC)))
+suppressWarnings(suppressPackageStartupMessages(library(reshape2)))
+suppressWarnings(suppressPackageStartupMessages(library(cowplot)))
+## We use this script to estimate the effectiveness of proportion methods
+
+## Load Conf
+args <- commandArgs(trailingOnly = TRUE)
+source(args[1])
+
+## Estimate cell type proportions
+est_prop <- music_prop(
+ bulk.eset = bulk_eset, sc.eset = scrna_eset,
+ clusters = celltypes_label,
+ samples = samples_label, select.ct = celltypes, verbose = T)
+
+
+## Show different in estimation methods
+## Jitter plot of estimated cell type proportions
+jitter.fig <- Jitter_Est(
+ list(data.matrix(est_prop$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 2cfd0db49bbc scripts/inspect.R
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/scripts/inspect.R Sun Sep 12 19:49:12 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 2cfd0db49bbc test-data/EMTABesethealthy.subset.rds
Binary file test-data/EMTABesethealthy.subset.rds has changed
diff -r 000000000000 -r 2cfd0db49bbc test-data/GSE50244bulkeset.subset.rds
Binary file test-data/GSE50244bulkeset.subset.rds has changed
diff -r 000000000000 -r 2cfd0db49bbc test-data/Mousebulkeset.rds
Binary file test-data/Mousebulkeset.rds has changed
diff -r 000000000000 -r 2cfd0db49bbc test-data/Mousesubeset.degenesonly2.half.rds
Binary file test-data/Mousesubeset.degenesonly2.half.rds has changed
diff -r 000000000000 -r 2cfd0db49bbc test-data/array.tsv
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/array.tsv Sun Sep 12 19:49:12 2021 +0000
@@ -0,0 +1,4 @@
+ Sample1 Sample2
+Gene1 1 3
+Gene2 2 4
+Gene3 3 5
diff -r 000000000000 -r 2cfd0db49bbc test-data/default_output.pdf
Binary file test-data/default_output.pdf has changed
diff -r 000000000000 -r 2cfd0db49bbc test-data/dendro.pdf
Binary file test-data/dendro.pdf has changed
diff -r 000000000000 -r 2cfd0db49bbc test-data/epith.markers
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/epith.markers Sun Sep 12 19:49:12 2021 +0000
@@ -0,0 +1,2614 @@
+Rp1
+Sox17
+1700034P13Rik
+Prex2
+Sulf1
+Xkr9
+Eya1
+Sbspon
+D030040B21Rik
+Crispld1
+Il17f
+Mcm3
+Kcnq5
+Col19a1
+Khdrbs2
+Bend6
+Gm37233
+Sema4c
+Fam178b
+Chst10
+Il1r2
+Il1rl1
+Gm37623
+Fhl2
+Gm29040
+Col3a1
+Stat4
+Gm28551
+Hecw2
+Ankrd44
+4930558J18Rik
+Aox2
+Als2cr12
+Cdk15
+Fzd7
+Icos
+Pard3bos3
+Nrp2
+Gm4208
+Klf7
+Cryga
+Fn1
+Tmem169
+Igfbp2
+Igfbp5
+6030407O03Rik
+Catip
+Slc11a1
+Prkag3
+Wnt6
+Wnt10a
+Des
+Tmem198
+BC035947
+Mogat1
+5730419F03Rik
+Serpine2
+Fam124b
+Dock10
+Pid1
+C130026I21Rik
+A530032D15Rik
+A530040E14Rik
+Sp110
+Sp100
+A630001G21Rik
+2810459M11Rik
+Kcnj13
+Inpp5d
+Ugt1a8
+Ugt1a6a
+Ugt1a1
+Gm29336
+4930434B07Rik
+Ackr3
+Gm28723
+Gm26683
+Agxt
+Pdcd1
+St8sia4
+Slco4c1
+Panct2
+Pam
+Gm29012
+Tnfrsf11a
+Serpinb2
+Cntnap5a
+Sctr
+Lypd1
+Tmem163
+Thsd7b
+C4bp
+Gm15848
+Ctse
+Tmcc2
+Gm19461
+Chil1
+Syt2
+Ptpn7
+Lmod1
+Gm38399
+Phlda3
+Igfn1
+Cacna1s
+Kif14
+Atp6v1g3
+Crb1
+Cfh
+B3galt2
+Rgs2
+Rgs18
+Ptgs2
+1700025G04Rik
+Ncf2
+Nmnat2
+Rgs16
+Cacna1e
+Ier5
+Tdrd5
+Nphs2
+Angptl1
+4930439D14Rik
+Astn1
+Pappa2
+Gm37083
+Fasl
+Dnm3os
+Gm16548
+Xcl1
+Rcsd1
+Cd247
+Fam78b
+Lrrc52
+Rxrg
+Rgs5
+Sh2d1b1
+Olfml2b
+Fcrla
+Gm38204
+Gm10522
+Fcgr4
+Pcp4l1
+Cd244
+Slamf7
+Cd48
+Cd84
+Slamf6
+Atp1a4
+Atp1a2
+Slamf8
+Apcs
+Aim2
+Gm4955
+BC094916
+Pydc3
+AI607873
+Ifi204
+Mndal
+Mnda
+Ifi203
+Ifi202b
+Ifi205
+Grem2
+Akt3
+2310043L19Rik
+Kif26b
+Lefty1
+1700047M11Rik
+Hlx
+Mark1
+Kcnk2
+Gm28172
+Prox1os
+Vash2
+Gm38037
+Rd3
+Kcnh1
+Sertad4
+Traf3ip3
+4930570N18Rik
+Lamb3
+Cd34
+Cr2
+Meig1
+Ccdc3
+Camk1d
+Proser2
+Proser21
+Itih2
+Itga8
+Vim
+Tmem236
+Mrc1
+Malrd1
+Nebl
+4930426L09Rik
+Armc3
+Tbpl2
+Il1f9
+Il1f5
+Il1rn
+Entpd8
+4933433C11Rik
+Sapcd2
+Fcnaos
+Obp2a
+Kcnt1
+1810012K08Rik
+Gm13563
+Notch1
+Egfl7
+Snhg7os
+Lcn4
+Stkld1
+Slc2a6
+Sardhos
+Col5a1
+Olfm1
+Ak8
+Pkn3
+Gm28035
+Gm14486
+Ptges
+Lcn2
+Gm13412
+St6galnac4
+Eng
+Phf19
+Stom
+Ggta1
+Gm13431
+Crb2
+Lhx2
+Lrp1b
+Kynu
+Gm13470
+Gm13499
+1700057H21Rik
+Neb
+Rprm
+Kcnj3
+Pla2r1
+Kcnh7
+Scn7a
+B3galt1
+Nostrin
+Gad1
+Rapgef4
+Gm28793
+Gm28230
+2600014E21Rik
+Ttc30a2
+Pde11a
+Itga4
+Prdx6b
+Fam171b
+Calcrl
+Tfpi
+Serping1
+Slc43a1
+Slc43a3
+Aplnr
+Creb3l1
+2900072N19Rik
+Gm13814
+Chst1
+Gm10804
+Gm13889
+E530001K10Rik
+Elf5
+Lmo2
+D430041D05Rik
+Pin1rt1
+Wt1
+Bdnf
+Gm13936
+3110099E03Rik
+Meis2
+2700033N17Rik
+Tmco5
+Rasgrp1
+Rad51
+Dll4
+Chac1
+Ehd4
+Stard9
+Epb42
+Map1a
+B2m
+Duox1
+Slc28a2
+AA467197
+Sema6d
+Slc12a1
+Fbn1
+Shc4
+Atp8b4
+Ncaph
+Kcnip3
+Acoxl
+Gm14029
+Tgm3
+Slc4a11
+Gfra4
+Adam33
+Siglec1
+Hspa12b
+Gm14102
+Bmp2
+Bfsp1
+Ralgapa2
+Thbd
+Cd93
+Gm21994
+Cst7
+Nanp
+Tcf15
+Defb36
+Rem1
+Id1
+Cox4i2
+Dusp15
+Ttll9
+Ccm2l
+Hck
+Necab3
+1700003F12Rik
+4930519P11Rik
+Gm14226
+2310005A03Rik
+Gssos2
+Gssos1
+Procr
+Gm16098
+Gm14168
+Myl9
+Tldc2
+Mroh8
+D630003M21Rik
+Lbp
+Snhg11
+Ptprt
+Tox2
+Jph2
+R3hdml
+Ada
+Kcns1
+Pltp
+Mmp9
+Slc12a5
+Cd40
+Cdh22
+Ocstamp
+Eya2
+Gm11464
+Gm11466
+Gm11468
+5031425F14Rik
+Prex1
+Kcnb1
+Gm14320
+Gm14235
+Tshz2
+Cass4
+Spo11
+Ctcfl
+Zbp1
+Zfp831
+Edn3
+Gm14434
+Sycp2
+Hrh3
+Gata5
+Col9a3
+Ptk6
+Srms
+BC051628
+Helz2
+Zbtb46
+Sox18
+Was
+Sytl5
+Tspan7
+Gm10489
+Nyx
+Gpr34
+Timp1
+Slc6a14
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diff -r 000000000000 -r 2cfd0db49bbc test-data/immune.markers
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/immune.markers Sun Sep 12 19:49:12 2021 +0000
@@ -0,0 +1,8126 @@
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diff -r 000000000000 -r 2cfd0db49bbc test-data/pheno.tsv
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/pheno.tsv Sun Sep 12 19:49:12 2021 +0000
@@ -0,0 +1,3 @@
+ gender type score
+Sample1 1 3 5
+Sample2 2 4 9