Mercurial > repos > bgruening > music_construct_eset

--- /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 @@
+<tool id="music_construct_eset" name="Construct Expression Set Object" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@"
+      profile="20.05" license="GPL-3.0-or-later" >
+    <description>Create an ExpressionSet object from tabular and textual data</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements" />
+    <command detect_errors="exit_code"><![CDATA[
+Rscript --vanilla '$conf'
+]]></command>
+    <configfiles>
+        <configfile name="conf" >
+
+suppressWarnings(suppressPackageStartupMessages(library(xbioc)))
+suppressWarnings(suppressPackageStartupMessages(library(MuSiC)))
+
+null_str_vec = function(gstr){
+   tokens = unlist(as.vector(strsplit(gstr, split=",")))
+   if (length(tokens) == 0){
+      return(NULL)
+   }
+   if (length(tokens) == 1){
+      return(tokens[[1]])
+   }
+   return(tokens)
+}
+
+## Assay Data
+## F rows of features and S columns of samples
+## - This file is the only non-optional parameter
+exprs_file = '$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')
+
+        </configfile>
+    </configfiles>
+    <inputs>
+        <param name="exprs_file" label="Assay Data" type="data" format="tabular,tsv"
+               help="F rows of features and S columns of samples. A Tab delimited file, with a header line and the first column has row names." />
+        <param name="pdata_file" label="Phenotype Data" type="data"
+               format="tabular,tsv" optional="true"
+               help="S rows of samples, and V columns of covariates (e.g. sex, age)" />
+        <param name="annotation" label="Annotation" type="text"
+               optional="true" help="A string detailing which chip was used"  >
+            <expand macro="validator_text_and_urls" />
+        </param>
+        <repeat name="metadata" title="Meta Data" min="0" max="15" >
+            <!-- optional, so min=0 -->
+            <param name="row_names" label="Label" type="text" >
+                <expand macro="validator_text_and_urls" />
+            </param>
+            <param name="label_desc" label="Label Description" type="text" >
+                <expand macro="validator_text_and_urls" />
+            </param>
+        </repeat>
+        <section name="expdata" title="Experiment Data" >
+            <param name="name" label="Experimenter Name" type="text" value="" optional="true" >
+                <expand macro="validator_text_and_urls" />
+            </param>
+            <param name="lab" label="Lab" type="text" value="" optional="true" >
+                <expand macro="validator_text_and_urls" />
+            </param>
+            <param name="contact" label="Contact" type="text" value="" optional="true" >
+                <expand macro="validator_text_and_urls" />
+            </param>
+            <param name="title" label="Title" type="text" value="" optional="true" >
+                <expand macro="validator_text_and_urls" />
+            </param>
+            <param name="abstract" label="Abstract" type="text" value="" optional="true" >
+                <expand macro="validator_text_and_urls" />
+            </param>
+            <param name="url" label="URL" type="text" value="" optional="true" >
+                <expand macro="validator_text_and_urls" />
+            </param>
+            <repeat name="other" title="Other Fields" min="1">
+                <param name="field" label="FieldName" type="text" value="notes" >
+                    <expand macro="validator_text_and_urls" />
+                </param>
+                <param name="comment" label="Comment" type="text" value="Created in Galaxy" >
+                    <expand macro="validator_text_and_urls" />
+                </param>
+            </repeat>
+        </section>
+    </inputs>
+    <outputs>
+        <data name="out_tab" format="tabular" label="${tool.name} on ${on_string}: General Info" />
+        <data name="out_rds" format="rdata.eset" label="${tool.name} on ${on_string}: RData ESet Object" />
+    </outputs>
+    <tests>
+        <test expect_num_outputs="2" >
+            <!-- Values from the manual -->
+            <param name="exprs_file" value="array.tsv" />
+            <param name="pdata_file" value="pheno.tsv" />
+            <param name="annotation" value="hgu95av2" />
+            <repeat name="metadata" >
+                <param name="row_names" value="gender" />
+                <param name="label_desc" value="Patient gender" />
+            </repeat>
+            <repeat name="metadata" >
+                <param name="row_names" value="type" />
+                <param name="label_desc" value="Case/control status" />
+            </repeat>
+            <repeat name="metadata" >
+                <param name="row_names" value="score" />
+                <param name="label_desc" value="Tumor Progress on XYZ scale" />
+            </repeat>
+            <section name="expdata">
+                <param name="name" value="Pierre Fermat" />
+                <param name="lab" value="Francis Galton Lab" />
+                <param name="contact" value="pfermat@lab.not.exist" />
+                <param name="title" value="Smoking-Cancer Experiment" />
+                <param name="abstract" value="An example ExpressionSet" />
+                <param name="url" value="www.lab.not.exist" />
+                <repeat name="other" >
+                    <param name="field" value="notes" />
+                    <param name="comment" value="Created in Galaxy" />
+                </repeat>
+                <repeat name="other" >
+                    <param name="field" value="general" />
+                    <param name="comment" value="Some other comment" />
+                </repeat>
+            </section>
+            <output name="out_tab">
+                <assert_contents>
+                    <has_text text="assayData: 3 features, 2 samples " />
+                </assert_contents>
+            </output>
+        </test>
+    </tests>
+    <help><![CDATA[
+Construct an ExpressionSet object from a variety of input attributes, such as experimentData, phenotype data, and annotations.
+
+For more options and information, consult `the manual <http://www.bioconductor.org/packages/release/bioc/vignettes/Biobase/inst/doc/ExpressionSetIntroduction.pdf>`_ and the `rdocumentation <https://www.rdocumentation.org/packages/Biobase/versions/2.32.0/topics/ExpressionSet>`_
+.
+    ]]></help>
+    <citations>
+        <citation type="bibtex">
+            @misc{falcon2007introduction,
+            title={An introduction to bioconductor’s expressionset class},
+            author={Falcon, Seth and Morgan, Martin and Gentleman, Robert},
+            year={2007}
+            }
+        </citation>
+    </citations>
+</tool>
\ No newline at end of file
--- /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 @@
+<macros>
+    <token name="@VERSION_SUFFIX@">0</token>
+    <!-- The ESet inspector/constructor and MuSiC tool can have
+         independent Galaxy versions but should reference the same
+         package version always. -->
+    <token name="@TOOL_VERSION@">0.1.1</token>
+    <xml name="requirements">
+        <requirements>
+            <requirement type="package" version="@TOOL_VERSION@" >music-deconvolution</requirement>
+            <requirement type="package" version="0.9.3" >r-cowplot</requirement>
+            <requirement type="package" version="1.4.4" >r-reshape2</requirement>
+        </requirements>
+    </xml>
+    <xml name="validator_index_identifiers" >
+        <validator type="regex" message="FORMAT terms separated by commas">^(([A-Za-z0-9+_ -]+)\s?,?)*$</validator>
+    </xml>
+    <xml name="validator_text" >
+        <validator type="regex" message="No commas allowed">^(([A-Za-z0-9+_ -]+)\s?)*$</validator>
+    </xml>
+    <xml name="celltypes_macro" >
+        <param name="celltypes" type="text" optional="true" value=""
+               label="Comma list of cell types to use from scRNA dataset" help="If NULL, then use all cell types." >
+            <expand macro="validator_index_identifiers" />
+        </param>
+    </xml>
+    <xml name="validator_text_and_urls" >
+        <validator type="regex" message="No commas or apostrophes allowed">^(([A-Za-z0-9+_ -@.:/]+)\s?)*$</validator>
+    </xml>
+</macros>
+
--- /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$M.theta + 1e-8)), method = "euclidean")
+## Hierarchical clustering using Complete Linkage
+hc2 <- hclust(d, method = "complete")
+## Plot the obtained dendrogram
+pdf(file = outfile_pdf, width = 8, height = 8)
+plot(hc2, cex = 0.6, hang = -1, main = "Cluster log(Mean of RA)")
+
+cl_type <- as.character(scrna_eset[[celltypes_label]])
+
+for (cl in seq_len(length(grouped_celltypes))) {
+  cl_type[cl_type %in% grouped_celltypes[[cl]]] <- names(grouped_celltypes)[cl]
+}
+pData(scrna_eset)[[clustertype_label]] <- factor(
+    cl_type, levels = c(names(grouped_celltypes),
+                        "CD-Trans", "Novel1", "Novel2"))
+
+est_bulk <- music_prop.cluster(
+    bulk.eset = bulk_eset, sc.eset = scrna_eset,
+    group.markers = marker_groups, clusters = celltypes_label,
+    groups = clustertype_label, samples = samples_label,
+    clusters.type = grouped_celltypes)
+
+write.table(est_bulk, file = outfile_tab, quote = F, col.names = NA, sep = "\t")
+dev.off()
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/scripts/estimateprops.R	Sun Sep 12 19:49:12 2021 +0000
@@ -0,0 +1,93 @@
+suppressWarnings(suppressPackageStartupMessages(library(xbioc)))
+suppressWarnings(suppressPackageStartupMessages(library(MuSiC)))
+suppressWarnings(suppressPackageStartupMessages(library(reshape2)))
+suppressWarnings(suppressPackageStartupMessages(library(cowplot)))
+## We use this script to estimate the effectiveness of proportion methods
+
+## Load Conf
+args <- commandArgs(trailingOnly = TRUE)
+source(args[1])
+
+## Estimate cell type proportions
+est_prop <- music_prop(
+    bulk.eset = bulk_eset, sc.eset = scrna_eset,
+    clusters = celltypes_label,
+    samples = samples_label, select.ct = celltypes, verbose = T)
+
+
+## Show different in estimation methods
+## Jitter plot of estimated cell type proportions
+jitter.fig <- Jitter_Est(
+    list(data.matrix(est_prop$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"))
+}
--- /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))
+}
Binary file test-data/EMTABesethealthy.subset.rds has changed
Binary file test-data/GSE50244bulkeset.subset.rds has changed
Binary file test-data/Mousebulkeset.rds has changed
Binary file test-data/Mousesubeset.degenesonly2.half.rds has changed
--- /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
Binary file test-data/default_output.pdf has changed
Binary file test-data/dendro.pdf has changed
--- /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
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--- /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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--- /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