Mercurial > repos > bgruening > music_compare
changeset 1:4447ed460308 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d007ae51743e621dc47524f681501e72ef3a2910"
| author | bgruening |
|---|---|
| date | Mon, 02 May 2022 09:58:49 +0000 |
| parents | 10bf0f89035f |
| children | 6c75960f6e56 |
| files | macros.xml music_compare.xml scripts/compare.R test-data/APOL1_Bulk.rds test-data/Control_Bulk.rds |
| diffstat | 5 files changed, 132 insertions(+), 86 deletions(-) [+] |
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--- a/macros.xml Thu Feb 10 12:53:49 2022 +0000 +++ b/macros.xml Mon May 02 09:58:49 2022 +0000 @@ -1,5 +1,5 @@ <macros> - <token name="@VERSION_SUFFIX@">3</token> + <token name="@VERSION_SUFFIX@">4</token> <!-- The ESet inspector/constructor and MuSiC tool can have independent Galaxy versions but should reference the same package version always. --> @@ -14,6 +14,7 @@ <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> + <requirement type="package" version="0.1_20">r-ggdendro</requirement> </requirements> </xml> <xml name="validator_index_identifiers" >
--- a/music_compare.xml Thu Feb 10 12:53:49 2022 +0000 +++ b/music_compare.xml Mon May 02 09:58:49 2022 +0000 @@ -31,6 +31,7 @@ </macros> <expand macro="requirements" /> <command detect_errors="exit_code" ><![CDATA[ +cat '$conf' >> /dev/stderr && mkdir report_data && Rscript --vanilla '$__tool_directory__/scripts/compare.R' '$conf' ]]></command> @@ -77,10 +78,11 @@ #end for ) -heat_grouped_p = as.logical('$heat_grouped_p') out_filt = list(cells = null_str_vec('$filter.out_list_cells'), facts = null_str_vec('$filter.out_list_facts')) + est_method = null_str_vec('$est_method') +dendro_setting = null_str_vec('$dendro_setting') out_heatmulti_pdf = '$out_heatmulti_pdf' out_heatsumm_pdf = '$out_heatsumm_pdf' @@ -132,7 +134,13 @@ <option value="MuSiC" selected="true" >MuSiC</option> <option value="NNLS" selected="true" >NNLS</option> </param> - <param name="heat_grouped_p" type="boolean" label="Individual heatmaps grouped by scRNA dataset?" checked="true" /> + <param name="dendro_setting" type="select" label="Cluster heatmaps?" + help="Samples, Cells and Datasets can all be clustered by similarity."> + <option value="None" selected="true" >No, preserve order of Rows and Columns</option> + <option value="Both">Cluster both Rows and Columns</option> + <option value="Cols">Cluster only Columns</option> + <option value="Rows">Cluster only Rows</option> + </param> <section name="filter" title="Filter Summary Plots" > <param name="out_list_cells" type="text" label="Show only these cell types (blank for all)" help="Comma-delimited list. Cell types given in the above scRNA datasets are still used for deconvolution (bulk reads are still assigned to discrete cell types), but we merely select the ones we want to show." /> @@ -155,7 +163,6 @@ <!-- NNLS Test with severe output filtering --> <expand macro="test_input" /> <param name="est_method" value="NNLS" /> - <param name="heat_grouped_p" value="true" /> <section name="filter" > <param name="out_list_cells" value="PT,Podo,Fib,Endo" /> <param name="out_list_facts" value="APOL1,Pheno1" /> @@ -166,7 +173,16 @@ <!-- NNLS Test with only factor filtering --> <expand macro="test_input" /> <param name="est_method" value="NNLS" /> - <param name="heat_grouped_p" value="true" /> + <section name="filter" > + <param name="out_list_facts" value="APOL1,Pheno1" /> + </section> + <output name="out_heatmulti_pdf" value="out_heat2.pdf" compare="sim_size" /> + </test> + <test expect_num_outputs="4" > + <!-- NNLS Test with factor filtering and dendrograms --> + <expand macro="test_input" /> + <param name="est_method" value="NNLS" /> + <param name="dendro_setting" value="Both" /> <section name="filter" > <param name="out_list_facts" value="APOL1,Pheno1" /> </section> @@ -176,7 +192,6 @@ <!-- MuSiC Test with no filtering --> <expand macro="test_input" /> <param name="est_method" value="MuSiC" /> - <param name="heat_grouped_p" value="true" /> <output_collection name="dtables" count="3"> <element name="Data Table" ftype="tabular" > <assert_contents>
--- a/scripts/compare.R Thu Feb 10 12:53:49 2022 +0000 +++ b/scripts/compare.R Mon May 02 09:58:49 2022 +0000 @@ -11,6 +11,7 @@ method_key <- list("MuSiC" = "est_music", "NNLS" = "est_nnls")[[est_method]] +delim <- "::" ## separator bulk datasets and their samples scale_yaxes <- function(gplot, value) { if (is.na(value)) { @@ -136,43 +137,6 @@ return(tab) } - -plot_grouped_heatmaps <- function(results) { - pdf(out_heatmulti_pdf, width = 8, height = 8) - for (sc_name in names(results)) { - named_list <- sapply( - names(results[[sc_name]]), - function(n) { - ## We transpose the data here, because - ## the plotting function omits by default - ## the Y-axis which are the samples. - ## Since the celltypes are the common factor - ## these should be the Y-axis instead. - t(data.matrix(results[[sc_name]][[n]][[method_key]])) - }, simplify = F, USE.NAMES = T) - named_methods <- names(results[[sc_name]]) - ## - plot_hmap <- Prop_heat_Est( - named_list, - method.name = named_methods) + - ggtitle(paste0("[", est_method, "] Cell type ", - "proportions of ", - "Bulk Datasets based on ", - sc_name, " (scRNA)")) + - xlab("Samples (Bulk)") + - ylab("Cell Types (scRNA)") + - theme(axis.text.x = element_text(angle = -90), - axis.text.y = element_text(size = 6)) - print(plot_hmap) - } - dev.off() -} - -## Desired plots -## 1. Pie chart: -## - Per Bulk dataset (using just normalised proportions) -## - Per Bulk dataset (multiplying proportions by nreads) - unlist_names <- function(results, method, prepend_bkname=FALSE) { unique(sort( unlist(lapply(names(results), function(scname) { @@ -181,7 +145,7 @@ if (prepend_bkname) { ## We *do not* assume unique bulk sample names ## across different bulk datasets. - res <- paste0(bkname, "::", res) + res <- paste0(bkname, delim, res) } return(res) }) @@ -201,7 +165,7 @@ ddff_scale <- data.frame() for (cell in all_celltypes) { for (sample in all_samples) { - group_sname <- unlist(strsplit(sample, split = "::")) + group_sname <- unlist(strsplit(sample, split = delim)) bulk <- group_sname[1] id_sample <- group_sname[2] for (scgroup in names(results)) { @@ -231,7 +195,7 @@ for (scgroup in names(results)) { for (bulkgroup in names(results[[scgroup]])) { dat <- results[[scgroup]][[bulkgroup]]$plot_groups - dat$Samples <- paste0(bulkgroup, "::", dat$Samples) #nolint + dat$Samples <- paste0(bulkgroup, delim, dat$Samples) #nolint res <- rbind(res, dat) } } @@ -247,7 +211,7 @@ bd_spread_scale <- list() bd_spread_prop <- list() for (bname in bulk_names) { - subs <- mat_names[startsWith(mat_names, paste0(bname, "::"))] + subs <- mat_names[startsWith(mat_names, paste0(bname, delim))] ## - bd[[bname]] <- rowSums(summat$prop[, subs]) bd_scale[[bname]] <- rowSums(summat$scaled[, subs]) @@ -260,8 +224,75 @@ prop = bd_spread_prop))) } -summarize_heatmaps <- function(grudat_spread_melt, do_factors) { - ## - +do_cluster <- function(grudat_spread_melt, xaxis, yaxis, value_name, + xlabs="", ylabs="", titled="", + order_col=T, order_row=T, size=11) { + + data_m <- grudat_spread_melt + data_matrix <- { + tmp <- dcast(data_m, formula(paste0(yaxis, " ~ ", xaxis)), value.var = value_name) + rownames(tmp) <- tmp[[yaxis]] + tmp[[yaxis]] <- NULL + tmp + } + dist_method <- "euclidean" + clust_method <- "complete" + + if (order_row) { + dd_row <- as.dendrogram(hclust(dist(data_matrix, method = dist_method), method = clust_method)) + row_ord <- order.dendrogram(dd_row) + ordered_row_names <- row.names(data_matrix[row_ord, ]) + data_m[[yaxis]] <- factor(data_m[[yaxis]], levels = ordered_row_names) + } + + if (order_col) { + dd_col <- as.dendrogram(hclust(dist(t(data_matrix), method = dist_method), + method = clust_method)) + col_ord <- order.dendrogram(dd_col) + ordered_col_names <- colnames(data_matrix[, col_ord]) + data_m[[xaxis]] <- factor(data_m[[xaxis]], levels = ordered_col_names) + } + + heat_plot <- ggplot(data_m, aes_string(x = xaxis, y = yaxis, fill = value_name)) + + geom_tile(colour = "white") + + scale_fill_gradient2(low = "steelblue", high = "red", mid = "white", + name = element_blank()) + + scale_y_discrete(position = "right") + + theme(axis.text.x = element_text(angle = -90, hjust = 0, + size = size)) + + ggtitle(label = titled) + xlab(xlabs) + ylab(ylabs) + + ## Graphics + dendro_linesize <- 0.5 + dendro_colunit <- 0.2 + dendro_rowunit <- 0.1 + final_plot <- heat_plot + + if (order_row) { + dendro_data_row <- ggdendro::dendro_data(dd_row, type = "rectangle") + dendro_row <- cowplot::axis_canvas(heat_plot, axis = "y", coord_flip = TRUE) + + ggplot2::geom_segment(data = ggdendro::segment(dendro_data_row), + ggplot2::aes(y = -y, x = x, xend = xend, yend = -yend), + size = dendro_linesize) + ggplot2::coord_flip() + final_plot <- cowplot::insert_yaxis_grob( + final_plot, dendro_row, grid::unit(dendro_colunit, "null"), + position = "left") + } + if (order_col) { + dendro_data_col <- ggdendro::dendro_data(dd_col, type = "rectangle") + dendro_col <- cowplot::axis_canvas(heat_plot, axis = "x") + + ggplot2::geom_segment(data = ggdendro::segment(dendro_data_col), + ggplot2::aes(x = x, y = y, xend = xend, yend = yend), + size = dendro_linesize) + final_plot <- cowplot::insert_xaxis_grob( + final_plot, dendro_col, grid::unit(dendro_rowunit, "null"), + position = "top") + } + return(cowplot::ggdraw(final_plot)) +} + +summarize_heatmaps <- function(grudat_spread_melt, do_factors, cluster="None") { + ## - Cluster is either "Rows", "Cols", "Both", or "None" do_single <- function(grudat_melted, yaxis, xaxis, fillval, title, ylabs = element_blank(), xlabs = element_blank(), use_log = TRUE, size = 11) { @@ -270,14 +301,22 @@ if (use_log) { melted[[fillval]] <- log10(melted[[fillval]] + 1) } - return(ggplot(melted) + - geom_tile(aes_string(y = yaxis, x = xaxis, fill = fillval), - colour = "white") + - scale_fill_gradient2(low = "steelblue", high = "red", - mid = "white", name = element_blank()) + - theme(axis.text.x = element_text(angle = -90, hjust = 0, - size = size)) + - ggtitle(label = title) + xlab(xlabs) + ylab(ylabs)) + if (cluster == "None") { + return(ggplot(melted) + + geom_tile(aes_string(y = yaxis, x = xaxis, fill = fillval), + colour = "white") + + scale_fill_gradient2( + low = "steelblue", high = "red", mid = "white", + name = element_blank()) + + theme(axis.text.x = element_text( + angle = -90, hjust = 0, size = size)) + + ggtitle(label = title) + xlab(xlabs) + ylab(ylabs)) + } else { + return(do_cluster(grudat_spread_melt, xaxis, yaxis, fillval, + xlabs, ylabs, title, + (cluster %in% c("Cols", "Both")), + (cluster %in% c("Rows", "Both")))) + } } do_gridplot <- function(title, xvar, plot="both", ncol=2, size = 11) { @@ -303,16 +342,16 @@ return(plot_grid(ggdraw() + draw_label(title, fontface = "bold"), plot_grid(plotlist = plist, ncol = ncol), ncol = 1, rel_heights = c(0.05, 0.95))) + } - } - p1 <- do_gridplot("Cell Types vs Bulk Datasets", "Bulk", "both", ) - p2a <- do_gridplot("Cell Types vs Samples", "Sample", "normal", 1, - size = 8) - p2b <- do_gridplot("Cell Types vs Samples (log10+1)", "Sample", "log", 1, - size = 8) + p1 <- do_gridplot("Cell Types vs Bulk Datasets", "Bulk", "both") + p2a <- do_gridplot("Cell Types vs Samples", "Sample", "normal", + ncol = 1, size = 8) + p2b <- do_gridplot("Cell Types vs Samples (log10+1)", "Sample", "log", + ncol = 1, size = 8) p3 <- ggplot + theme_void() if (do_factors) { - p3 <- do_gridplot("Cell Types against Factors", "Factors", "both") + p3 <- do_gridplot("Cell Types vs Factors", "Factors", "both") } return(list(bulk = p1, samples = list(log = p2b, normal = p2a), @@ -346,8 +385,8 @@ ylab("Bulk Dataset") } - title_a <- "Cell Types against Bulk" - title_b <- "Bulk Datasets against Cells" + title_a <- "Cell Types vs Bulk Datasets" + title_b <- "Bulk Datasets vs Cell Types" if (do_factors) { title_a <- paste0(title_a, " and Factors") title_b <- paste0(title_b, " and Factors") @@ -380,31 +419,28 @@ return(grudat_filt) } +writable2 <- function(obj, prefix, title) { + write.table(obj, + file = paste0("report_data/", prefix, "_", + title, ".tabular"), + quote = F, sep = "\t", col.names = NA) +} + results <- music_on_all(files) - -if (heat_grouped_p) { - plot_grouped_heatmaps(results) -} else { - plot_all_individual_heatmaps(results) -} - -save.image("/tmp/sesh.rds") - summat <- summarized_matrix(results) grudat <- group_by_dataset(summat) grudat_spread_melt <- merge_factors_spread(grudat$spread, flatten_factor_list(results)) +grudat_spread_melt_filt <- filter_output(grudat_spread_melt, out_filt) - +plot_all_individual_heatmaps(results) ## The output filters ONLY apply to boxplots, since these take do_factors <- (length(unique(grudat_spread_melt[["Factors"]])) > 1) - -grudat_spread_melt_filt <- filter_output(grudat_spread_melt, out_filt) - -heat_maps <- summarize_heatmaps(grudat_spread_melt_filt, do_factors) box_plots <- summarize_boxplots(grudat_spread_melt_filt, do_factors) +heat_maps <- summarize_heatmaps(grudat_spread_melt_filt, do_factors, + dendro_setting) pdf(out_heatsumm_pdf, width = 14, height = 14) print(heat_maps) @@ -417,12 +453,6 @@ stats_scale <- lapply(grudat$spread$scale, function(x) { t(apply(x, 1, summary))}) -writable2 <- function(obj, prefix, title) { - write.table(obj, - file = paste0("report_data/", prefix, "_", - title, ".tabular"), - quote = F, sep = "\t", col.names = NA) -} ## Make the value table printable grudat_spread_melt$value.scale <- as.integer(grudat_spread_melt$value.scale) # nolint colnames(grudat_spread_melt) <- c("Sample", "Cell", "Bulk", "Factors",