Mercurial > repos > bgruening > music_inspect_eset

changeset 0:2fed32b5aa02 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 08c6fd3885bdfbf8b5c3f4dcc2d04729b577e3e1"
author bgruening
date Sun, 12 Sep 2021 19:48:26 +0000
parents
children 817eb707bbf4
files inspect_eset.xml macros.xml scripts/dendrogram.R scripts/estimateprops.R scripts/inspect.R test-data/EMTABesethealthy.subset.rds test-data/GSE50244bulkeset.subset.rds test-data/Mousebulkeset.rds test-data/Mousesubeset.degenesonly2.half.rds test-data/array.tsv test-data/default_output.pdf test-data/dendro.pdf test-data/epith.markers test-data/immune.markers test-data/pheno.tsv
diffstat 15 files changed, 11077 insertions(+), 0 deletions(-) [+]
line wrap: on
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/inspect_eset.xml	Sun Sep 12 19:48:26 2021 +0000
@@ -0,0 +1,99 @@
+<tool id="music_inspect_eset" name="Inspect Expression Set Object" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@"
+      profile="20.05" license="GPL-3.0-or-later" >
+    <description>Inspect an ExpressionSet object by a variety of attributes</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements"/>
+    <command detect_errors="exit_code"><![CDATA[
+Rscript --vanilla '$__tool_directory__/scripts/inspect.R' '$conf'
+]]></command>
+    <configfiles>
+        <configfile name="conf" >
+
+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)
+}
+
+rds_eset = readRDS('$rds_eset')
+inspector = null_str_vec('$inspector')
+outfile_tab='$out_tab'
+
+        </configfile>
+    </configfiles>
+    <inputs>
+        <param name="rds_eset" label="ESet Dataset" type="data" format="rdata.eset" />
+        <param name="inspector" label="Inspect" type="select"
+               help="Inspect an aspect of the ESet dataset" >
+            <!-- See: https://www.rdocumentation.org/packages/Biobase/versions/2.32.0/topics/eSet -->
+            <option value="print" selected="true">General Information</option>
+            <option value="exprs" >Expression Data Table</option>
+            <option value="pData" >PhenoType Data Table</option>
+            <option value="fData" >Feature Data Table</option>
+            <option value="dims" >Dimension</option>
+            <option value="experimentData" />
+            <option value="signature" />
+            <option value="annotation" />
+            <option value="abstract" />
+        </param>
+    </inputs>
+    <outputs>
+        <data name="out_tab" format="tabular" label="${tool.name} on ${on_string}: Inspection Result" />
+    </outputs>
+    <tests>
+        <test expect_num_outputs="1" >
+            <!-- Inspect 0 -->
+            <param name="rds_eset" value="EMTABesethealthy.subset.rds" />
+            <param name="inspector" value="print" />
+            <output name="out_tab" >
+                <assert_contents>
+                    <has_text text="sampleNames: AZ_A10 AZ_A11 ... HP1502401_K15 (250 total)" />
+                </assert_contents>
+            </output>
+        </test>
+        <test expect_num_outputs="1" >
+            <!-- Inspect 1 -->
+            <param name="rds_eset" value="EMTABesethealthy.subset.rds" />
+            <param name="inspector" value="pData" />
+            <output name="out_tab" >
+                <assert_contents>
+                    <has_n_columns n="5" />
+                    <has_text_matching expression="AZ_A10\s+1\s+Non T2D\s+1\s+5\s+delta" />
+                </assert_contents>
+            </output>
+        </test>
+        <test expect_num_outputs="1" >
+            <!-- Inspect 2 -->
+            <param name="rds_eset" value="EMTABesethealthy.subset.rds" />
+            <param name="inspector" value="dims" />
+            <output name="out_tab" >
+                <assert_contents>
+                    <has_n_columns n="1" />
+                    <has_text_matching expression="Samples\s+\d{1,4}"/>
+                </assert_contents>
+            </output>
+        </test>
+    </tests>
+    <help><![CDATA[
+Inspect an ExpressionSet object by a variety of 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 19:48:26 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 19:48:26 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$M.theta + 1e-8)), method = "euclidean")
+## Hierarchical clustering using Complete Linkage
+hc2 <- hclust(d, method = "complete")
+## Plot the obtained dendrogram
+pdf(file = outfile_pdf, width = 8, height = 8)
+plot(hc2, cex = 0.6, hang = -1, main = "Cluster log(Mean of RA)")
+
+cl_type <- as.character(scrna_eset[[celltypes_label]])
+
+for (cl in seq_len(length(grouped_celltypes))) {
+  cl_type[cl_type %in% grouped_celltypes[[cl]]] <- names(grouped_celltypes)[cl]
+}
+pData(scrna_eset)[[clustertype_label]] <- factor(
+    cl_type, levels = c(names(grouped_celltypes),
+                        "CD-Trans", "Novel1", "Novel2"))
+
+est_bulk <- music_prop.cluster(
+    bulk.eset = bulk_eset, sc.eset = scrna_eset,
+    group.markers = marker_groups, clusters = celltypes_label,
+    groups = clustertype_label, samples = samples_label,
+    clusters.type = grouped_celltypes)
+
+write.table(est_bulk, file = outfile_tab, quote = F, col.names = NA, sep = "\t")
+dev.off()
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/scripts/estimateprops.R	Sun Sep 12 19:48:26 2021 +0000
@@ -0,0 +1,93 @@
+suppressWarnings(suppressPackageStartupMessages(library(xbioc)))
+suppressWarnings(suppressPackageStartupMessages(library(MuSiC)))
+suppressWarnings(suppressPackageStartupMessages(library(reshape2)))
+suppressWarnings(suppressPackageStartupMessages(library(cowplot)))
+## We use this script to estimate the effectiveness of proportion methods
+
+## Load Conf
+args <- commandArgs(trailingOnly = TRUE)
+source(args[1])
+
+## Estimate cell type proportions
+est_prop <- music_prop(
+    bulk.eset = bulk_eset, sc.eset = scrna_eset,
+    clusters = celltypes_label,
+    samples = samples_label, select.ct = celltypes, verbose = T)
+
+
+## Show different in estimation methods
+## Jitter plot of estimated cell type proportions
+jitter.fig <- Jitter_Est(
+    list(data.matrix(est_prop$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 19:48:26 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 19:48:26 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 19:48:26 2021 +0000
@@ -0,0 +1,2614 @@
+Rp1
+Sox17
+1700034P13Rik
+Prex2
+Sulf1
+Xkr9
+Eya1
+Sbspon
+D030040B21Rik
+Crispld1
+Il17f
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+Kcnq5
+Col19a1
+Khdrbs2
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+Sctr
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+Thsd7b
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+Cd34
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+Pde11a
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/immune.markers	Sun Sep 12 19:48:26 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 19:48:26 2021 +0000
@@ -0,0 +1,3 @@
+	gender	type	score
+Sample1	1	3	5
+Sample2	2	4	9