edited the description and reading ads files ( id it is in a directory)

R/read_asd_summar.R

@@ -1,115 +1,116 @@
 #' Read ASD Spectral Files and Create a SummarizedExperiment Object
-#' 
-#' This function will read a single or multiple ASD files and extracts the spectral data 
-#' and associated metadata, combines them into a "SummarizedExperiment" object. This object 
+#'
+#' This function will read a single or multiple ASD files and extracts the spectral data
+#' and associated metadata, combines them into a "SummarizedExperiment" object. This object
 #' contains the spectral data as an assay matrix and metadata about the samples and wavelengths.
 #'
 #' @name read_asd_summar
 #' @title Read the ASD files and return as SummarizedExperiment object.
-#' 
+#'
 #' @param path A character string specifying the path to a directory containing the ".asd" files or a single
 #'             ".asd" file.
-#'             
+#'
 #' @return A `SummarizedExperiment` object containing:
 #'   \itemize{
 #'     \item{\code{assays}}{A list with a single assay matrix named \code{counts},
 #'       where rows represent wavelengths and columns represent different samples.}
 #'     \item{\code{colData}}{A `DataFrame` with sample metadata, including the sample names.}
 #'     \item{\code{rowData}}{A `DataFrame` with wavelength information.}
 #'   }
-#'   
+#'
 #' @details
 #' This function uses 2 functions such as "read.asd" and "extract.metadata" from the package "FieldSpectra"
 #' to read the data and metadata from the given files. This function will then uses the data from the files
 #' and make a SummarizedExperiment object out of it which can be used for further data analysis.
-#' 
+#'
 #' @import FieldSpectra
 #' @import SummarizedExperiment
-#' 
-#' 
-#' @author Methun George, Steffen Neumann
-#' 
+#'
+#'
+#' @author Methun George, Dr.Steffen Neumann
+#'
 #' @examples
 #' # path <- "path/to/your/asd/files"
 #' # se <- read_asd_summar(path)
 #' # se
 #' # colnames(se)
 #' # rownames(se)
-#' 
+#'
 #' @export
 
 
 library(FieldSpectra)
 library(SummarizedExperiment)
 
-read_asd_summar <- function(path) {
-  path_info <- file.info(path)
-  if (path_info$isdir) {
-    asd_files <- list.files(path = path, pattern = "\\.asd$", full.names = TRUE)
-  } else {
-    asd_files <- path
-  }
-
+
+  read_asd_summar <- function(path) {
+    if (length(path) == 1 && file.info(path)$isdir) {
+      asd_files <- list.files(path = path, pattern = "\\.asd$", full.names = TRUE)
+    } else {
+      asd_files <- path
+    }
+
+
   # Initialize lists to store the data frame and metadata
   asd_data_list <- list()
   asd_metadata_list <- list()
   assay_data <- list()
-  
+
   # Loop over each file and read it (in case of directory)
   for (file in asd_files) {
     asd_data <- read.asd(file.dir = file, out.dir = '~')
     wavelengths <- asd_data$Wavelength
     spectra <- asd_data$Spectra
-    
+
     # Store data for the assay matrix
     assay_data[[basename(file)]] <- spectra
     combined_data <- data.frame(wavelengths, spectra)
     asd_data_list[[basename(file)]] <- combined_data
-    
+
     # Extract the metadata
     asd_metadata <- extract.metadata(file.dir = file,  out.dir = '~' ,instrument = "ASD")
     file_name <- asd_metadata$Spectra_File_Name
     spectral_time <- asd_metadata$Spectrum_Time_UTC
     combined_metadata <- data.frame(file_name, spectral_time)
     asd_metadata_list <- append(asd_metadata_list, list(combined_metadata))
   }
-  
+
   # Combine metadata for better readability
   asd_metadata_list <- do.call(rbind, asd_metadata_list)
-  
+
   # Initialize the assay matrix data frame
   assay_matrix <- do.call(cbind, assay_data)
   wavelengths <- asd_data_list[[1]]$wavelengths
   rownames(assay_matrix) <- wavelengths
   assay_df <- data.frame(assay_matrix)
-  
+
   # Set column names based on file names from metadata
   colnames(assay_df) <- sapply(asd_metadata_list$file_name, function(x) basename(x))
-  
+
   # Create ColData
   colData <- DataFrame(samplenames = colnames(assay_df))
-  
+
   # Create rowData
   rowData <- DataFrame(Wavelengths = rownames(assay_df))
-  
+
   # Create the SummarizedExperiment object
   se <- SummarizedExperiment(assays = list(counts = as.matrix(assay_df)),
                              colData = colData,
                              rowData = rowData)
-  
+
   return(se)
 }
 
-# Example 
+# Example
 # path <- "/Users/methungeorge/Desktop/IPB/test/data"
 # se <- read_asd_summar(path)
 # se
-
-# # Check the SummarizedExperiment object
+#
+# # # Check the SummarizedExperiment object
 # print(se)
 # colnames(se)
 # rownames(se)
-# # Access the assay data
+# # # Access the assay data
 # assay_data <- assay(se, "counts")
 # head(assay_data)
 ##note : now the coldata is 1D and we need to include the trait information, eg look at the article

R/read_sig_summar.R

@@ -3,7 +3,7 @@
 #' This function reads .sig files from a specified directory or a file path, extracts wavelength and reflectance data,
 #' and combines them into a \code{SummarizedExperiment} object. Each .sig file is expected to contain reflectance data
 #' and a sample name in its content.
-#' 
+#'
 #' @name read_sig_summar
 #' @title Read the SIG files and return as SummarizedExperiment object.
 #'
@@ -31,8 +31,8 @@
 #' print(se)
 #'
 #' @import SummarizedExperiment
-#' @author Methun George, Steffen Neumann
-#' 
+#' @author Methun George, Dr.Steffen Neumann
+#'
 #' @export
 
 library(SummarizedExperiment)
@@ -46,55 +46,55 @@ read_sig_to_se <- function(path) {
   } else {
     sig_files <- path
   }
-  
+
   # Create an empty list to store data frames and sample names
   all_data <- list()
   sample_names <- c()
-  
+
   # Read each file and extract data
   for (file in sig_files) {
     file_content <- readLines(file)
-    
+
     # Extract sample name
     name_line <- grep("^name=", file_content, value = TRUE)
     if (length(name_line) > 0) {
       sample_name <- sub("^name=", "", name_line)
     } else {
-      sample_name <- basename(file) 
+      sample_name <- basename(file)
     }
     sample_names <- c(sample_names, sample_name)
-    
+
     # Extract data (reflectance %)
     data_start <- grep("^data=", file_content)
     data_lines <- file_content[(data_start + 1):length(file_content)]
     data <- read.table(text = data_lines, header = FALSE, fill = TRUE)
-    
+
     # Select columns for wavelengths and reflectance
     data <- data[, c(1, 4)]
     colnames(data) <- c("Wavelengths(nm)", sample_name)
-    
+
     # Add the data frame to the list
     all_data[[sample_name]] <- data
   }
-  
+
   # Combine all data frames by wavelengths
   combined_data <- Reduce(function(x, y) merge(x, y, by = "Wavelengths(nm)", all = TRUE), all_data)
-  
+
   # Set row names to wavelengths and remove the "Wavelengths(nm)" column
   rownames(combined_data) <- combined_data$`Wavelengths(nm)`
-  combined_data <- combined_data[, -1, drop = FALSE]  
-  
+  combined_data <- combined_data[, -1, drop = FALSE]
+
   # Create colData
   colData <- DataFrame(sampleNames = colnames(combined_data))
-  
+
   # Create rowData
   rowData <- DataFrame(Wavelengths = rownames(combined_data))
-  
+
   # Create the SummarizedExperiment object
   se <- SummarizedExperiment(assays = list(counts = as.matrix(combined_data)),
                              colData = colData,
                              rowData = rowData)
-  
+
   return(se)
 }