diff scripts/dendrogram.R @ 0:22232092be53 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d007ae51743e621dc47524f681501e72ef3a2910"

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/scripts/dendrogram.R	Mon May 02 09:59:18 2022 +0000
@@ -0,0 +1,132 @@
+##
+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, check.names = FALSE,
+                      stringsAsFactors = FALSE)$V1)
+}
+
+args <- commandArgs(trailingOnly = TRUE)
+source(args[1])
+
+
+## Perform the estimation
+## Produce the first step information
+sub.basis <- music_basis(scrna_eset, clusters = celltypes_label,
+                         samples = samples_label,
+                         select.ct = celltypes)
+
+## Plot the dendrogram of design matrix and cross-subject mean of
+## realtive abundance
+## Hierarchical clustering using Complete Linkage
+d1 <- dist(t(log(sub.basis$Disgn.mtx + 1e-6)), method = "euclidean")
+hc1 <- hclust(d1, method = "complete")
+## Hierarchical clustering using Complete Linkage
+d2 <- dist(t(log(sub.basis$M.theta + 1e-8)), method = "euclidean")
+hc2 <- hclust(d2, method = "complete")
+
+
+if (length(data.to.use) > 0) {
+    ## We then perform bulk tissue cell type estimation with pre-grouping
+    ## of cell types: C, list_of_cell_types, marker genes name, marker
+    ## genes list.
+    ## data.to.use = list(
+    ##     "C1" = list(cell.types = c("Neutro"),
+    ##                 marker.names=NULL,
+    ##                 marker.list=NULL),
+    ##     "C2" = list(cell.types = c("Podo"),
+    ##                 marker.names=NULL,
+    ##                 marker.list=NULL),
+    ##     "C3" = list(cell.types = c("Endo","CD-PC","LOH","CD-IC","DCT","PT"),
+    ##                 marker.names = "Epithelial",
+    ##                 marker.list = read_list("../test-data/epith.markers")),
+    ##     "C4" = list(cell.types = c("Macro","Fib","B lymph","NK","T lymph"),
+    ##                 marker.names = "Immune",
+    ##                 marker.list = read_list("../test-data/immune.markers"))
+    ## )
+    grouped_celltypes <- lapply(data.to.use, function(x) {
+        x$cell.types
+    })
+    marker_groups <- lapply(data.to.use, function(x) {
+        x$marker.list
+    })
+    names(marker_groups) <- names(data.to.use)
+
+
+    cl_type <- as.character(scrna_eset[[celltypes_label]])
+
+    for (cl in seq_len(length(grouped_celltypes))) {
+        cl_type[cl_type %in%
+                grouped_celltypes[[cl]]] <- names(grouped_celltypes)[cl]
+    }
+    pData(scrna_eset)[[clustertype_label]] <- factor(
+        cl_type, levels = c(names(grouped_celltypes),
+                            "CD-Trans", "Novel1", "Novel2"))
+
+    est_bulk <- music_prop.cluster(
+        bulk.eset = bulk_eset, sc.eset = scrna_eset,
+        group.markers = marker_groups, clusters = celltypes_label,
+        groups = clustertype_label, samples = samples_label,
+        clusters.type = grouped_celltypes
+    )
+
+    estimated_music_props <- est_bulk$Est.prop.weighted.cluster
+    ## NNLS is not calculated here
+
+    ## Show different in estimation methods
+    ## Jitter plot of estimated cell type proportions
+    methods_list <- c("MuSiC")
+
+    jitter_fig <- Jitter_Est(
+        list(data.matrix(estimated_music_props)),
+        method.name = methods_list, title = "Jitter plot of Est Proportions",
+        size = 2, alpha = 0.7) +
+        theme_minimal() +
+        labs(x = element_blank(), y = element_blank()) +
+        theme(axis.text = element_text(size = 6),
+              axis.text.x = element_blank(),
+              legend.position = "none")
+
+    plot_box <- Boxplot_Est(list(
+        data.matrix(estimated_music_props)),
+        method.name = methods_list) +
+        theme_minimal() +
+        labs(x = element_blank(), y = element_blank()) +
+        theme(axis.text = element_text(size = 6),
+              axis.text.x = element_blank(),
+              legend.position = "none")
+
+    plot_hmap <- Prop_heat_Est(list(
+        data.matrix(estimated_music_props)),
+        method.name = methods_list) +
+        labs(x = element_blank(), y = element_blank()) +
+        theme(axis.text.y = element_text(size = 6),
+              axis.text.x = element_text(angle = -90, size = 5),
+              plot.title = element_text(size = 9),
+              legend.key.width = unit(0.15, "cm"),
+              legend.text = element_text(size = 5),
+              legend.title = element_text(size = 5))
+
+}
+    
+pdf(file = outfile_pdf, width = 8, height = 8)
+par(mfrow = c(1, 2))
+plot(hc1, cex = 0.6, hang = -1, main = "Cluster log(Design Matrix)")
+plot(hc2, cex = 0.6, hang = -1, main = "Cluster log(Mean of RA)")
+if (length(data.to.use) > 0) {
+    plot_grid(jitter_fig, plot_box, plot_hmap, ncol = 2, nrow = 2)
+}
+message(dev.off())
+
+if (length(data.to.use) > 0) {
+    write.table(estimated_music_props,
+                file = outfile_tab, quote = F, col.names = NA, sep = "\t")
+}