address lintr errors

tools/celesta/celesta_assign_cells.R

@@ -1,5 +1,5 @@
 # ---------------------------------------------------------------------------------
-# The main algorithim for CELESTA cell type assignment 
+# The main algorithim for CELESTA cell type assignment
 # ---------------------------------------------------------------------------------
 
 suppressWarnings(suppressMessages(library(janitor)))
@@ -13,77 +13,77 @@ suppressWarnings(suppressMessages(library(reshape2)))
 suppressWarnings(suppressMessages(library(zeallot)))
 suppressWarnings(suppressMessages(library(CELESTA)))
 
-### Define command line arguments 
-option_list = list(
-  make_option(c("-i", "--imagingdata"), action="store", default=NA, type='character',
-              help="Path to imaging data"),
-  make_option(c("-p", "--prior"), action="store", default=NA, type='character',
-              help="Path to prior marker info file"),
-  make_option(c("-x", "--xcol"), action="store", default=NA, type='character',
-            help="Name of column in adata.obs containing X coordinate"),
-  make_option(c("-y", "--ycol"), action="store", default=NA, type='character',
-            help="Name of column in adata.obs containing Y coordinate"),
-  make_option(c("--filter"), action="store_true", type='logical', default=FALSE,
+### Define command line arguments
+option_list <- list(
+  make_option(c("-i", "--imagingdata"), action = "store", default = NA, type = "character",
+              help = "Path to imaging data"),
+  make_option(c("-p", "--prior"), action = "store", default = NA, type = "character",
+              help = "Path to prior marker info file"),
+  make_option(c("-x", "--xcol"), action = "store", default = NA, type = "character",
+              help = "Name of column in adata.obs containing X coordinate"),
+  make_option(c("-y", "--ycol"), action = "store", default = NA, type = "character",
+              help = "Name of column in adata.obs containing Y coordinate"),
+  make_option(c("--filter"), action = "store_true", type = "logical", default = FALSE,
               help="Boolean to filter cells or not (default: no filtering)"),
-  make_option(c("--highfilter"), action="store", default=0.9, type='double',
-              help="High marker threshold if filtering cells (default: 0.9)"),
-  make_option(c("--lowfilter"), action="store", default=0.4, type='double',
-              help="Low marker threshold if filtering cells (default: 0.4)"),
-  make_option(c("--maxiteration"), action="store", default=10, type='integer',
-              help="Maximum iterations allowed in the EM algorithm per round"),
-  make_option(c("--changethresh"), action="store", default=0.01, type='double',
-              help="Ending condition for the EM algorithm"),    
-  make_option(c("--highexpthresh"), action="store", default='default_high_thresholds', type='character',
-            help="Path to file specifying high expression thresholds for anchor and index cells"),
-  make_option(c("--lowexpthresh"), action="store", default='default_low_thresholds', type='character',
-            help="Path to file specifying low expression thresholds for anchor and index cells")
+  make_option(c("--highfilter"), action = "store", default = 0.9, type = "double",
+              help = "High marker threshold if filtering cells (default: 0.9)"),
+  make_option(c("--lowfilter"), action = "store", default = 0.4, type = "double",
+              help = "Low marker threshold if filtering cells (default: 0.4)"),
+  make_option(c("--maxiteration"), action = "store", default = 10, type = "integer",
+              help = "Maximum iterations allowed in the EM algorithm per round"),
+  make_option(c("--changethresh"), action = "store", default = 0.01, type = "double",
+              help = "Ending condition for the EM algorithm"), 
+  make_option(c("--highexpthresh"), action = "store", default = "default_high_thresholds", type = "character",
+              help = "Path to file specifying high expression thresholds for anchor and index cells"),
+  make_option(c("--lowexpthresh"), action = "store", default = "default_low_thresholds", type = "character",
+              help = "Path to file specifying low expression thresholds for anchor and index cells")
 )
 
-### Functions 
-anndata_to_celesta <- function(input_adata, x_col, y_col) { 
+### Functions
+anndata_to_celesta <- function(input_adata, x_col, y_col) {
 
   #' Function to convert anndata object to dataframe readable by CELESTA
-  #' Coordinates columns in adata.obs are renamed to 'X' and 'Y', and placed at beginning of dataframe 
+  #' Coordinates columns in adata.obs are renamed to "X" and "Y", and placed at beginning of dataframe
   #' Marker intensities are concatted columnwise to the X and Y coords. cols: X,Y,Marker_1,...Marker N
 
   # initialize output as dataframe from adata.obs
   celesta_input_dataframe <- data.frame(input_adata$obs)
 
-  # subset to X and Y coordinates from obs only 
+  # subset to X and Y coordinates from obs only
   celesta_input_dataframe <- celesta_input_dataframe %>% 
-      dplyr::select({{x_col}},{{y_col}})
+    dplyr::select({{x_col}}, {{y_col}})
 
-  # rename X,Y column names to what CELESTA wants 
-  colnames(celesta_input_dataframe) <- c('X','Y')
+  # rename X,Y column names to what CELESTA wants
+  colnames(celesta_input_dataframe) <- c("X", "Y")
 
   # merge X,Y coords with marker intensities from adata.X
   x_df <- data.frame(input_adata$X)
   colnames(x_df) <- input_adata$var_names
-  celesta_input_dataframe <- cbind(celesta_input_dataframe,x_df)
+  celesta_input_dataframe <- cbind(celesta_input_dataframe, x_df)
 
   return(celesta_input_dataframe)
 }
 
-### Main 
-# parse args 
-opt = parse_args(OptionParser(option_list=option_list))
+### Main
+# parse args
+opt <- parse_args(OptionParser(option_list = option_list))
 
-# read anndata, convert to celesta format 
+# read anndata, convert to celesta format
 adata <- read_h5ad(opt$imagingdata)
 celesta_input_df <- anndata_to_celesta(adata, x_col = opt$xcol, y_col = opt$ycol)
 
-# read prior marker info 
+# read prior marker info
 prior <- read.csv(opt$prior, check.names = FALSE)
 
-# clean prior names, keeping a copy of originals for writing output 
+# clean prior names, keeping a copy of originals for writing output
 prior_original_names <- colnames(prior)
 prior <- janitor::clean_names(prior, case = "all_caps")
 
-# clean input dataframe names, keeping a copy of originals for writing output 
+# clean input dataframe names, keeping a copy of originals for writing output
 celesta_input_df_original_names <- colnames(celesta_input_df)
 celesta_input_df <- janitor::clean_names(celesta_input_df, case = "all_caps")
 
-# instantiate celesta object 
+# instantiate celesta object
 CelestaObj <- CreateCelestaObject(
   project_title = "",
   prior_marker_info = prior,
@@ -101,58 +101,58 @@ if (opt$filter) {
   print("Proceeding to cell type assignment without cell filtering")
 }
 
-# check for non-default expression threshold files 
-if (opt$highexpthresh != 'default_high_thresholds') {
-  # read high thresholds 
+# check for non-default expression threshold files
+if (opt$highexpthresh != "default_high_thresholds") {
+  # read high thresholds
   print("Using custom high expression thresholds")
   high_expression_thresholds <- read.csv(opt$highexpthresh)
-  high_expression_threshold_anchor <- high_expression_thresholds$anchor
-  high_expression_threshold_index <- high_expression_thresholds$index
+  hi_exp_thresh_anchor <- high_expression_thresholds$anchor
+  hi_exp_thresh_index <- high_expression_thresholds$index
 } else {
   print("Using default high expression thresholds -- this may need adjustment") 
-  high_expression_threshold_anchor <- rep(0.7,length = 50)
-  high_expression_threshold_index <- rep(0.5,length = 50)
+  hi_exp_thresh_anchor <- rep(0.7, length = 50)
+  hi_exp_thresh_index <- rep(0.5, length = 50)
 }
 
-if (opt$lowexpthresh != 'default_low_thresholds') {
-  # read low thresholds 
+if (opt$lowexpthresh != "default_low_thresholds") {
+  # read low thresholds
   print("Using custom low expression thresholds")
   low_expression_thresholds <- read.csv(opt$highexpthresh)
-  low_expression_threshold_anchor <- low_expression_thresholds$anchor
-  low_expression_threshold_index <- low_expression_thresholds$index
+  low_exp_thresh_anchor <- low_expression_thresholds$anchor
+  low_exp_thresh_index <- low_expression_thresholds$index
 } else {
   print("Using default low expression thresholds") 
-  low_expression_threshold_anchor <- rep(0.9,length = 50)
-  low_expression_threshold_index <- rep(1,length = 50)
+  low_exp_thresh_anchor <- rep(0.9, length = 50)
+  low_exp_thresh_index <- rep(1, length = 50)
 }
 
-# run cell type assignment 
+# run cell type assignment
 CelestaObj <- AssignCells(CelestaObj,
-  max_iteration = opt$maxiteration,
-  cell_change_threshold = opt$changethresh,
-  high_expression_threshold_anchor = high_expression_threshold_anchor,
-  low_expression_threshold_anchor = low_expression_threshold_anchor,
-  high_expression_threshold_index = high_expression_threshold_index,
-  low_expression_threshold_index = low_expression_threshold_index,
-  save_result = FALSE)
-
-# save object as an RDS file for cell type plotting 
-# for the time being, this is not exposed to Galaxy 
+                          max_iteration = opt$maxiteration,
+                          cell_change_threshold = opt$changethresh,
+                          high_expression_threshold_anchor = hi_exp_thresh_anchor,
+                          low_expression_threshold_anchor = low_exp_thresh_anchor,
+                          high_expression_threshold_index = hi_exp_thresh_index,
+                          low_expression_threshold_index = low_exp_thresh_index,
+                          save_result = FALSE)
+
+# save object as an RDS file for cell type plotting
+# for the time being, this is not exposed to Galaxy
 saveRDS(CelestaObj, file = "celestaobj.rds")
 
-# rename celesta assignment columns so they're obvious in output anndata 
+# rename celesta assignment columns so they are obvious in output anndata
 celesta_assignments <- CelestaObj@final_cell_type_assignment
 celesta_assignments <- janitor::clean_names(celesta_assignments)
 colnames(celesta_assignments) <- paste0("celesta_", colnames(celesta_assignments))
 
 # merge celesta assignments into anndata object
 adata$obs <- cbind(adata$obs,celesta_assignments)
 
-# print cell type value_counts to standard output 
-print('----------------------------------------')
-print('Final cell type counts')
+# print cell type value_counts to standard output
+print("----------------------------------------")
+print("Final cell type counts")
 print(adata$obs %>% dplyr::count(celesta_final_cell_type, sort = TRUE))
-print('----------------------------------------')
+print("----------------------------------------")
 
-# write output anndata file 
-write_h5ad(adata, 'result.h5ad')
+# write output anndata file
+write_h5ad(adata, "result.h5ad")

tools/celesta/celesta_plot_cells.R

@@ -1,5 +1,5 @@
 # ---------------------------------------------------------------------------------
-# Plot assigned cell type combinations with CELESTA 
+# Plot assigned cell type combinations with CELESTA
 # ---------------------------------------------------------------------------------
 
 suppressWarnings(suppressMessages(library(janitor)))
@@ -13,64 +13,64 @@ suppressWarnings(suppressMessages(library(reshape2)))
 suppressWarnings(suppressMessages(library(zeallot)))
 suppressWarnings(suppressMessages(library(CELESTA)))
 
-# define command line args 
-option_list = list(
-  make_option(c("-r", "--rds"), action="store", default='celestaobj.rds', type='character',
-              help="Path to CelestaObj RDS"),
-  make_option(c("-p", "--prior"), action="store", default=NA, type='character',
-              help="Path to prior marker info file"),
-  make_option(c("-c", "--celltypes"), action="store", default=NA, type='character',
-              help="Comma-separated list of cell types to plot"),
-  make_option(c("-s", "--size"), action="store", default=1, type='double',
-              help="Point size for plotting"),
-  make_option(c("--width"), action="store", default=12, type='integer',
-              help="Width of plot (inches)"),
-  make_option(c("--height"), action="store", default=12, type='integer',
-              help="Height of plot (inches)"),
-  make_option(c("--dpi"), action="store", default=300, type='integer',
-              help="DPI (dots per inch) of plot")
+# define command line args
+option_list <- list(
+  make_option(c("-r", "--rds"), action = "store", default = "celestaobj.rds", type = "character",
+              help = "Path to CelestaObj RDS"),
+  make_option(c("-p", "--prior"), action = "store", default = NA, type = "character",
+              help = "Path to prior marker info file"),
+  make_option(c("-c", "--celltypes"), action = "store", default = NA, type = "character",
+              help = "Comma-separated list of cell types to plot"),
+  make_option(c("-s", "--size"), action = "store", default = 1, type = "double",
+              help = "Point size for plotting"),
+  make_option(c("--width"), action = "store", default = 12, type = "integer",
+              help = "Width of plot (inches)"),
+  make_option(c("--height"), action = "store", default = 12, type = "integer",
+              help = "Height of plot (inches)"),
+  make_option(c("--dpi"), action = "store", default = 300, type = "integer",
+              help = "DPI (dots per inch) of plot")
 )
 
-# parse args 
-opt = parse_args(OptionParser(option_list=option_list))
+# parse args
+opt <- parse_args(OptionParser(option_list = option_list))
 
 CelestaObj <- readRDS(opt$rds)
 cell_types_to_plot <- strsplit(opt$celltypes, ",")[[1]]
 
-# read prior marker info 
-prior <- read.csv(opt$prior,row.names = 1)
+# read prior marker info
+prior <- read.csv(opt$prior, row.names = 1)
 
-# get indices of cell types to plot from the prior marker table 
+# get indices of cell types to plot from the prior marker table
 cell_type_indices <- which(row.names(prior) %in% cell_types_to_plot) 
 
 print(cell_types_to_plot)
 print(cell_type_indices)
 
 print(row.names(prior))
 
-# create output directory if it doesn't already exist 
-dir.create('cell_assign_plots')
+# create output directory if it doesn"t already exist
+dir.create("cell_assign_plots")
 
-# create the cell type plot 
+# create the cell type plot
 g <- PlotCellsAnyCombination(cell_type_assignment_to_plot=CelestaObj@final_cell_type_assignment[,(CelestaObj@total_rounds+1)],
-                        coords = CelestaObj@coords,
-                        prior_info = prior_marker_info,
-                        cell_number_to_use=cell_type_indices,
-                        test_size=1,
-                        save_plot = FALSE)
+                            coords = CelestaObj@coords,
+                            prior_info = prior_marker_info,
+                            cell_number_to_use=cell_type_indices,
+                            test_size=1,
+                            save_plot = FALSE)
 
-# create a unique output name for the plot based on the input cell types 
+# create a unique output name for the plot based on the input cell types
 cell_types_cleaned <- paste(make_clean_names(cell_types_to_plot), collapse = "")
 output_name <- paste(c("plot_cells_",cell_types_cleaned,".png"), collapse = "")
 
-# save to subdir 
-# FIXME: may want to expose plotting params to galaxy 
+# save to subdir
+# FIXME: may want to expose plotting params to galaxy
 ggsave(
-    path = 'cell_assign_plots',
-    filename = output_name,
-    plot = g,
-    width = opt$width,
-    height = opt$height,
-    units = "in",
-    dpi = opt$dpi
-)
+  path = "cell_assign_plots",
+  filename = output_name,
+  plot = g,
+  width = opt$width,
+  height = opt$height,
+  units = "in",
+  dpi = opt$dpi
+)