Merge pull request #56 from brownmp/devel

Created one annotation covariate bar for rows

Former-commit-id: a05bac8
Former-commit-id: b17476a

R/NextGenHeatMap.R

@@ -84,21 +84,13 @@ Create_NGCHM <- function(infercnv_obj,
  }
 
  ## set variables 
- reference_idx = row.names(plot_data[unlist(infercnv_obj@reference_grouped_cell_indices),])
  ref_index = infercnv_obj@reference_grouped_cell_indices
- ref_groups = names(infercnv_obj@reference_grouped_cell_indices)
+ reference_idx = row.names(plot_data[unlist(ref_index),])
+ ref_groups = names(ref_index)
 
  # ---------------------- Import Dendrogram & Order Rows -----------------------------------------------------------------------------------
  # IF Cluster By Group is set to TRUE:
  # Get the order of the rows (cell lines) from the dendrogram created by infer_cnv 
- #
-
- ## import and read the dendrogram for the observed data created using the ape library
- #den_path <- paste(out_dir, "observations_dendrogram.txt", sep=.Platform$file.sep)
- #phylo <- ape::read.tree(file = den_path)
- # if multiphylo trees, need to iterate to get to labels 
- #obs_order <- rev(unlist(lapply(1:length(phylo), function(x) phylo[[x]]$tip.label))) # vector holding cell line order taken from the dendrogram
-
 
  # read the file containing the groupings created by infer_cnv
  row_groups_path <- paste(out_dir, "observation_groupings.txt", sep=.Platform$file.sep)
@@ -213,75 +205,63 @@ Create_NGCHM <- function(infercnv_obj,
  display = "visible",
  thickness = as.integer(20))
 
- # Covariate bar for annotation groups 
+ # Covariate to identify Reference and Observed data
  annotation_col <- as.character(unlist(row_groups["Annotation.Color"])) # group colors
  annotation_group <- as.character(unlist(row_groups["Annotation.Group"]))# group number
  names(annotation_group) <- cells
  names(annotation_col) <- cells
- annotation_palette <- get_group_color_palette()(length(unique(annotation_group)))
  annotation_unique_group <- unique(annotation_group)
- ## create color mapping
- colMap_annotation <- NGCHM::chmNewColorMap(values = as.vector(annotation_unique_group), # row names are the cells 
- colors = annotation_palette,
- missing.color = "white")
- annotation_cov <- NGCHM::chmNewCovariate(fullname = 'Annotation', 
- values = annotation_group, 
- value.properties = colMap_annotation,
- type = "discrete")
- hm <- NGCHM::chmAddCovariateBar(hm, "row", annotation_cov, 
- display = "visible", 
- thickness = as.integer(20))
- # Covariate to identify Reference and Observed data
 
- cell_type <- replace(row_order, 1:length(row_order) %in% unlist(infercnv_obj@observation_grouped_cell_indices), paste("Observed"))
+ len <-lengths(ref_index)
+ ref_bar_labels <- unlist(sapply(1:length(len), function(x){ rep(ref_groups[x],len[x]) }))
+ names(ref_bar_labels) <- reference_idx
 
- ref_groups = names(infercnv_obj@reference_grouped_cell_indices)
+ # if you want the exact coloring as the original inferCNV plots 
+ #annotation_palette <- c(get_group_color_palette()(length(ref_index)), get_group_color_palette()(length(annotation_unique_group)))
 
- ## Label the references based on index locations 
- if (length(ref_groups) > 1) {
- for(i in 1:length(ref_groups)){ 
- cell_type <- replace(cell_type, infercnv_obj@reference_grouped_cell_indices[[i]], paste("Reference",toString(i),sep = "")) 
- }
- } else {
- for(i in 1:length(ref_groups)){ 
- cell_type <- replace(cell_type, 1:length(cell_type) %in% infercnv_obj@reference_grouped_cell_indices[[1]], paste("Reference"))
- }
- }
- # make a new variable for later use that has the cell type and cell ID as the name 
- ## cell ID's need to map to cell types 
- names(cell_type) <- row_order
+ # combine reference and observed labels 
+ annotation_group <- c(ref_bar_labels,annotation_group)
+
+ # change the observed group names in bar to group namnes 
+ observed_data <- infercnv_obj@observation_grouped_cell_indices
+ lapply(1:length(observed_data), function(x) { 
+ tmp <- names(observed_data[x])
+ annotation_group <<- replace(annotation_group, observed_data[[x]], tmp) } )
+ unique_group <- unique(annotation_group)
+ annotation_palette <- get_group_color_palette()(length(unique_group))
 
- # check if all reference cells are in cell type 
- if (!(all(reference_idx %in% names(cell_type)))){
- missing_refs <- reference_idx[which(!(reference_idx %in% names(cell_type)))]
+ # check if all reference cells are included 
+ if (!(all(reference_idx %in% names(annotation_group)))){
+ missing_refs <- reference_idx[which(!(reference_idx %in% names(annotation_group)))]
  error_message <- paste("Error: Not all references are accounted for.",
  "Make sure the reference names match the names in the data.\n",
  "Check the following reference cell lines: ", 
  paste(missing_refs, collapse = ","))
  stop(error_message)
  }
- if (!is.null(cell_type)){
- ## unique group names 
- types <- unique(cell_type)
- ## create colors for groups 
- type_palette <- get_group_color_palette()(length(types))
- names(type_palette) <- types 
-
- colMap_type <- NGCHM::chmNewColorMap(values = types, 
- names = types,
- colors = type_palette,
- missing.color = "white", 
- type = "linear")
-
- type_cov <- NGCHM::chmNewCovariate(fullname = 'Cell Type', 
- values = cell_type, 
- value.properties = colMap_type,
- type = "discrete")
- hm <- NGCHM::chmAddCovariateBar(hm, "row", type_cov, 
- display = "visible", 
- thickness = as.integer(20))
+ # check if all observed cells are included
+ observed_idx <- row.names(plot_data[unlist(infercnv_obj@observation_grouped_cell_indices),])
+ if (!(all(observed_idx %in% names(annotation_group)))){
+ missing_obs <- reference_idx[which(!(observed_idx %in% names(annotation_group)))]
+ error_message <- paste("Error: Not all observed cell lines are accounted for.",
+ "Make sure the reference names match the names in the data.\n",
+ "Check the following reference cell lines: ", 
+ paste(missing_obs, collapse = ","))
+ stop(error_message)
  }
 
+ ## create color mapping
+ colMap_annotation <- NGCHM::chmNewColorMap(values = as.vector(unique_group), 
+ colors = annotation_palette,
+ missing.color = "white")
+ annotation_cov <- NGCHM::chmNewCovariate(fullname = 'Annotation', 
+ values = annotation_group, 
+ value.properties = colMap_annotation,
+ type = "discrete")
+ hm <- NGCHM::chmAddCovariateBar(hm, "row", annotation_cov, 
+ display = "visible", 
+ thickness = as.integer(20))
+
  #---------------------------------------Export the heat map-----------------------------------------------------------------------------------------------------------------------
  ## adjust the size of the heat map 
  #hm@width <- as.integer(500)