138 lines
3.6 KiB
R
138 lines
3.6 KiB
R
# .utilities.R
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#
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# Miscellaneous R code to suppport the project
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#
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# Version: 1.2
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# Date: 2017 09
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# Author: Boris Steipe
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#
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# V 1.2 update database utilities to support 2017 version of JSON sources
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# V 1.1 2017 updates for ABC-units
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# V 1.0 First code
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#
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# ToDo:
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# Notes:
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#
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# ==============================================================================
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# ====== SCRIPTS =============================================================
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source("./scripts/ABC-dbUtilities.R")
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# ====== SUPPORT FUNCTIONS =====================================================
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objectInfo <- function(x) {
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# Function to combine various information items about R objects
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#
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# Input: an R object
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# Value: none - prints information as side-effect
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cat("object contents:")
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print(x, digits = 22) # print value at maximal precision
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cat("\nstructure of object:\n")
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str(x)
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if (! is.list(x)) { # Don't use cat() if x is a list. cat() can't handle lists.
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cat("\nmode: ", mode(x), "\n")
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cat("typeof: ", typeof(x), "\n")
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cat("class: ", class(x), "\n")
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}
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# if the object has attributes, print them too
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if (! is.null(attributes(x))) {
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cat("\nattributes:\n")
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attributes(x)
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}
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# Done
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}
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biCode <- function(s) {
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# make a 5 character code from a binomial name by concatening
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# the first three letter of the first word and the first
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# two letters of the second word.
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#
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# There are many ways to do this, here we assemble the two parts
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# in a loop, this way the function is vectorized and can
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# work on a large vector of names.
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b <- character()
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for (i in 1:length(s)) {
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b[i] <- sprintf("%s%s",
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toupper(unlist(substr(s[i], 1, 3))),
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toupper(unlist(substr(strsplit(s[i], "\\s+")[[1]][2],
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1, 2))))
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}
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return(b)
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}
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pBar <- function(i, l, nCh = 50) {
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# Draw a progress bar in the console
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# i: the current iteration
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# l: the total number of iterations
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# nCh: width of the progress bar
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ticks <- round(seq(1, l-1, length.out = nCh))
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if (i < l) {
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if (any(i == ticks)) {
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p <- which(i == ticks)
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p1 <- paste(rep("#", p), collapse = "")
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p2 <- paste(rep("-", nCh - p), collapse = "")
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cat(sprintf("\r|%s%s|", p1, p2))
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flush.console()
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}
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}
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else { # done
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cat("\n")
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}
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}
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waitTimer <- function(t, nIntervals = 50) {
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# pause and wait for t seconds and display a progress bar as
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# you are waiting
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t <- as.numeric(t)
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if (t < 0.1) {return(invisible())}
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increment <- t / nIntervals
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bar <- "----:----|" # One module for the progress bar:
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bar <- rep(bar, ceiling(nIntervals / 10)) # repeat,
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bar <- unlist(strsplit(bar, "")) # split into single characters,
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bar <- bar[1:nIntervals] # truncate,
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bar <- paste(bar, collapse="") # and collapse.
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cat(sprintf("\nWaiting: |%s\n |", bar))
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for (i in 1:(nIntervals - 1)) {
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Sys.sleep(increment)
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cat("=")
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}
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Sys.sleep(increment)
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cat("|\n\n")
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return(invisible())
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}
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# ====== DATA ==================================================================
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# 10 species of fungi for reference analysis.
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# http://steipe.biochemistry.utoronto.ca/abc/index.php/Reference_species_for_fungi
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REFspecies <- c("Aspergillus nidulans",
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"Bipolaris oryzae",
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"Coprinopsis cinerea",
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"Cryptococcus neoformans",
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"Neurospora crassa",
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"Puccinia graminis",
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"Saccharomyces cerevisiae",
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"Schizosaccharomyces pombe",
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"Ustilago maydis",
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"Wallemia mellicola"
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)
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# [END]
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