Merge pull request #92 from morinlab/kdreval-dev

init prettyCoOncoplot

DESCRIPTION

@@ -46,7 +46,8 @@ Imports:
     SRAdb,
     stats,
     tidyverse,
-    workflowr
+    workflowr,
+    ggpubr
 Remotes: morinlab/g3viz
 VignetteBuilder: knitr
 Depends:

NAMESPACE

@@ -71,6 +71,7 @@ export(plot_sample_circos)
 export(populate_each_tool_result)
 export(populate_tool_results)
 export(prettyChromoplot)
+export(prettyCoOncoplot)
 export(prettyForestPlot)
 export(prettyOncoplot)
 export(prettyRainfallPlot)
@@ -104,10 +105,12 @@ import(dbplyr)
 import(dplyr)
 import(g3viz)
 import(ggplot2)
+import(ggpubr)
 import(ggrepel)
 import(ggsci)
 import(ggthemes)
 import(grid)
+import(maftools)
 import(metaviz)
 import(reshape2)
 import(rtracklayer)

R/database.R

@@ -1093,8 +1093,10 @@ get_cn_states = function(regions_list,
   cn_matrix = pivot_wider(all_cn, id_cols = "sample_id", names_from = "region_name", values_from = "CN") %>%
     column_to_rownames("sample_id")
 
+  names(cn_matrix) = region_names
+
   #order the regions the same way the user provided them for convenience
-  return(cn_matrix[,region_names])
+  return(cn_matrix)
 }
 
 

R/utilities.R

@@ -1725,11 +1725,11 @@ get_gambl_colours = function(classification = "all",
                             "NEG" = "#E5A4CB")
 
   all_colours[["BL"]] = c("M53-BL" = "#A6CEE3",
-                          "DLBCL-1" = "#721F0F",
+                          "DLBCL-A" = "#721F0F",
                           "IC-BL" = "#45425A",
                           "DGG-BL" = "#E90C8BFF",
-                          "DLBCL-2" = "#FB9A99",
-                          "DLBCL-3" = "#C41230")
+                          "DLBCL-B" = "#FB9A99",
+                          "DLBCL-C" = "#C41230")
 
   all_colours[["FL"]] = c(dFL = "#99C1B9", cFL = "#D16666", DLBCL = "#479450")
 

R/viz.R

@@ -1624,6 +1624,137 @@ prettyOncoplot = function(maftools_obj,
 }
 
 
+#' Display 2 prettyOncoplots side-by-side.
+#'
+#' `prettyCoOncoplot` returns ggplot-compatible figure of 2 prettyOncoplots side-by-side.
+#'
+#' This function will generate a graphic displaying 2 oncoplots side-by-side. Optionally user can
+#' annotate each oncoplot with it's own title that will be displayed at the top. All the arguments
+#' recognized by prettyOncoplot are supported and can be specified when calling this function.
+#' For both oncoplots the same specified parameters will be applied (e.g. genes to display, split columns,
+#' font size, top annotation etc). If the provided argument is not recognized by prettyOncoplot,
+#' it will be discarded. If you want a specific order of oncoplots on the left and right, please
+#' ensure the argument `comparison_column` is a factor with first level being the group
+#' you want to be plotted on the left side. For developers: new arguments added to prettyOncoplot in the future
+#' are expected to be out-of-the-box compatible with this function nd would not need code modifications.
+#'
+#' @param maf Required argument. A maftools object containing the mutations you want to plot on both oncoplots.
+#' @param metadata Required argument. A data.frame with metadata for both oncoplots.
+#' @param comparison_values Optional: If the comparison column contains more than two values or is not a factor, specify a character vector of length two in the order you would like the factor levels to be set, reference group first.
+#' @param comparison_column Required: the name of the metadata column containing the comparison values.
+#' @param label1 Optional argument. Label to be shown as a title for the oncoplot #1.
+#' @param label2 Optional argument. Label to be shown as a title for the oncoplot #2.
+#'
+#' @return A ggplot object with 2 oncoplots side-by-side.
+#' @export
+#' @import ComplexHeatmap ggpubr maftools
+#'
+#' @examples
+#' ssm=get_coding_ssm(limit_cohort = c("BL_Adult", "BL_Pediatric"))
+#' ssm=maftools::read.maf(ssm)
+#' meta=get_gambl_metadata() %>% dplyr::filter(cohort %in% c("BL_Adult", "BL_Pediatric"))
+#' prettyCoOncoplot(maf=ssm,
+#'     metadata = meta,
+#'     comparison_column = "cohort",
+#'     include_noncoding = NULL,
+#'     minMutationPercent = 0,
+#'     genes=c("MYC", "TET2", "TP53", "DDX3X", "ID3"),
+#'     metadataColumns=c("pathology", "EBV_status_inf", "pairing_status", "cohort"),
+#'     splitColumnName="EBV_status_inf",
+#'     metadataBarHeight=10,
+#'     fontSizeGene=12,
+#'     metadataBarFontsize=10,
+#'     label1="Adult",
+#'     label2="Pediatric")
+#'
+prettyCoOncoplot <-   function(maf,
+                               metadata,
+                               comparison_column,
+                               comparison_values,
+                               label1,
+                               label2,
+                               ...) {
+    # check for required arguments
+    required = c("maf", "metadata", "comparison_column")
+
+    defined = names(as.list(match.call())[-1])
+
+    if (any(!required %in% defined)) {
+      stop("Please provide mutation data and metadata for 2 pretty Oncoplots with specified comparison_column.")
+    }
+
+    #If no comparison_values are specified, derive the comparison_values from the specified comparison_column
+    if(missing(comparison_values)){
+      if(class(metadata[[comparison_column]]) == "factor"){
+        comparison_values = levels(metadata[[comparison_column]])
+      } else {
+        comparison_values = unique(metadata[[comparison_column]])
+      }
+    }
+
+    #Ensure there are only two comparison_values
+    {
+      if(length(comparison_values) != 2)
+        stop(paste0("Your comparison must have two values. \nEither specify comparison_values as a vector of length 2 or subset your metadata so your comparison_column has only two unique values or factor levels."))
+    }
+
+    #Subset the metadata to the specified comparison_values and the maf to the remaining sample_ids
+    meta1 = metadata[metadata[[comparison_column]] %in% comparison_values[1], ]
+    meta2 = metadata[metadata[[comparison_column]] %in% comparison_values[2], ]
+
+    # Subset maf to only samples in the comparison values
+    ssm1 = maftools::subsetMaf(maf,tsb=pull(meta1, Tumor_Sample_Barcode))
+    ssm2 = maftools::subsetMaf(maf,tsb=pull(meta2, Tumor_Sample_Barcode))
+
+    # Arguments to pass into prettyOncoplot
+    oncoplot_args = list(...)
+    # Discard any arguments not supported by prettyOncoplot
+    oncoplot_args = oncoplot_args[names(oncoplot_args) %in% intersect(names(oncoplot_args),
+                                                                      formalArgs(prettyOncoplot))]
+    # Build oncoplot No1
+    op1 = do.call(prettyOncoplot, c(
+      list(
+        maftools_obj = ssm1,
+        these_samples_metadata = meta1
+      ),
+      oncoplot_args
+    ))
+    # convert it to ggplot object
+    op1 = grid.grabExpr(draw(op1), width = 10, height = 17)
+    # if user provided annotation label, place it as a name for oncoplot No1
+    if (!missing(label1)) {
+      op1 = annotate_figure(op1,
+                            top = text_grob(label1,
+                                            face = "bold",
+                                            size = 20))
+    }
+    # Build oncoplot No2
+    op2 = do.call(prettyOncoplot, c(
+      list(
+        maftools_obj = ssm2,
+        these_samples_metadata = meta2
+      ),
+      oncoplot_args
+    ))
+    # convert it to ggplot object
+    op2 = grid.grabExpr(draw(op2), width = 10, height = 17)
+    # if user provided annotation label, place it as a name for oncoplot No2
+    if (!missing(label2)) {
+      op2 = annotate_figure(op2,
+                            top = text_grob(label2,
+                                            face = "bold",
+                                            size = 20))
+    }
+    # arrange 2 oncoplots together side by side
+    p = ggarrange(op1,
+                  op2,
+                  ncol = 2,
+                  nrow = 1)
+
+    return(p)
+  }
+
+
 #' Generate a colourful multi-panel overview of hypermutation in regions of interest across many samples.
 #'
 #' @param regions_bed Bed file with chromosome coordinates, should contain columns chr, start, end, name (with these exact names).