Example R code

galaxy_column

#!/usr/bin/env Rscript

# -----
# USAGE
# -----

# ./galaxy_column ~/desktop/galaxy1014.txt SVZ_conf_lo DG_conf_hi

# ---------
# FUNCTIONS
# ---------

# read a table in tab-delimited format from a particular file
#
# * file - a file or pipe to read the table from
read.galaxy_tabular = function(file) {
  read.table(file, header = TRUE, sep = "\t", fill = TRUE, as.is = TRUE)
}

# write data to a file in Excel-friendly format (CSV) from a particular frame
#
# * file - a file or pipe to read the table from
# * frame - data structure to write
write.excel = function(file, frame) write.csv(frame, file, row.names = FALSE)

# open a pipe representing the clipboard
clipboard.out = function() pipe('pbcopy', 'w')

# given a pipe, use it in the callback and then close it afterwards
#
# * p - pipe or file to use
# * callback - action to perform before closing the pipe
pipe.close_after = function(p, callback) {
  callback(p)
  close(p)
}

# ----
# MAIN
# ----

# read in a table name and two column names
args = commandArgs(TRUE)
table_name = args[1]
a = args[2]
b = args[3]

# read in a table from the table name
table = read.galaxy_tabular(table_name)

# create a new column by dividing column a and b and returning 'TRUE' if > 2
new_column = table[a] / table[b] > 2.0

# write the new column to the clipboard in Excel-friendly format
pipe.close_after( clipboard.out(), function(p) write.excel(p, new_column) )

cat('output a new column to the clipboard for pasting into excel\n')

galaxy_filter

#!/usr/bin/env Rscript

# -----
# USAGE
# -----

# ./galaxy_filter ~/desktop/galaxy1014.txt 'M/P > 2'

# ---------
# FUNCTIONS
# ---------

# filter down a list of rows
#
# * f - function with one parameter, "row". If returns false, row is removed
# * x - the table to filter
filter = function(f, x) {
  ind = as.logical( sapply(x, f) )

  x[ !is.na(ind) & ind ]
}

# read a table in tab-delimited format from a particular file
#
# * file - a file or pipe to read the table from
read.galaxy_tabular = function(file) {
  read.table(file, header = TRUE, sep = "\t", fill = TRUE, as.is = TRUE)
}

# write data to a file in Excel-friendly format (CSV) from a particular frame
#
# * file - a file or pipe to read the table from
# * frame - data structure to write
write.excel <- function(file, frame) {
  write.csv(frame, file, row.names = FALSE)
}

# open a pipe representing the clipboard
clipboard.out <- function() pipe('pbcopy', 'w');

# given a pipe, use it in the callback and then close it afterwards
#
# * p - pipe or file to use
# * callback - action to perform before closing the pipe
pipe.close_after <- function(p, callback) {
  callback(p);
  close(p);
}

# ----
# MAIN
# ----

# read in the table name and column to filter by
args = commandArgs(TRUE)
table_name = args[1]
a = args[2]

# read in a table given the provided table name
table = read.galaxy_tabular(table_name)

# filter rows out of the table depending on the values in column
table2 = filter(function(row) { row[a] == 'TRUE' }, table)

# write the new table to the clipboard in Excel format
pipe.close_after( clipboard.out(), function(p) write.excel(p, table2) )

cat('output a new column to the clipboard for pasting into excel\n')