comparison w4mcorcov_wrapper.R @ 6:7bd523ca1f9a draft

planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit cafda5095a79ce2376325b57337302f95137195d

5:50f60f94c034

## log file
##---------

my_log <- function(x, ...) { cat(paste(iso8601.znow(), " ", x, ..., nl, sep=""))}
my_fatal <- function(x, ...) { 
  my_log("ERROR: ", x, ...)
  quit(save = "no", status = 11, runLast = TRUE)
}

my_log("Start of the '", modNamC, "' Galaxy module call: ")

my_env$facC               <- as.character(argVc["facC"])
my_env$pairSigFeatOnly    <- as.logical(argVc["pairSigFeatOnly"])
my_env$levCSV             <- as.character(argVc["levCSV"])
my_env$matchingC          <- as.character(argVc["matchingC"])
my_env$labelFeatures      <- as.character(argVc["labelFeatures"]) # number of features to label at each extreme of the loadings or 'ALL'

label_features <- my_env$labelFeatures
labelfeatures_check <- TRUE
if ( is.na(label_features) ) {
  labelfeatures_check <- FALSE

  # receiver for result of the call to corcov_calc
  my_result <- NULL

  # compute and plot the correlation_vs_covariance details plot
  #   The parameter settings here are generally taken from bioconductor ropls::plot.opls source.
  marVn <- c(4.6, 4.1, 2.6, 1.6)
  old_par <- par(
    font      = 2         # bold font face
  , font.axis = 2         # bold font face for axis
  , font.lab  = 2         # bold font face for x and y labels
  , lwd       = 2         # line-width - interpretation is device spcific
  , mar       = marVn     # margins
  , pch       = 18        # black diamond plot-character, see help for graphics::points
  # , mfrow     = c(2,2)    # two rows by two columns
  , pty       = "s"       # force plots to be square
  )
  plot2pdf(
    file.name = my_env$contrast_detail
  , width  = 8
  , height = 8
  , plot.function = function() {
      # plot layout four plots per page
      layout(matrix(1:4, byrow = TRUE, nrow = 2))
      my_result <<- corcov_calc(
          calc_env            = my_env
        , failure_action      = my_fatal
        , progress_action     = my_log
        , corcov_tsv_action   = corcov_tsv_action
        , salience_tsv_action = salience_tsv_action
        )
    }
  )
  par(old_par)
  
  my_log( "--------------------------  Finished data processing  --------------------------")
}

my_log( "End of the '", modNamC, "' Galaxy module call")

6:7bd523ca1f9a

## log file
##---------

my_log <- function(x, ...) { cat(paste(iso8601.znow(), " ", x, ..., nl, sep=""))}
my_fatal <- function(x, ...) {
  my_log("ERROR: ", x, ...)
  quit(save = "no", status = 11, runLast = TRUE)
}

my_log("Start of the '", modNamC, "' Galaxy module call: ")

my_env$facC               <- as.character(argVc["facC"])
my_env$pairSigFeatOnly    <- as.logical(argVc["pairSigFeatOnly"])
my_env$levCSV             <- as.character(argVc["levCSV"])
my_env$matchingC          <- as.character(argVc["matchingC"])
my_env$labelFeatures      <- as.character(argVc["labelFeatures"]) # number of features to label at each extreme of the loadings or 'ALL'
my_env$cplot_o            <- as.logical(argVc["cplot_o"]) # TRUE if orthogonal C-plot is requested
my_env$cplot_p            <- as.logical(argVc["cplot_p"]) # TRUE if parallel C-plot is requested
my_env$cplot_y            <- as.character(argVc["cplot_y"]) # Choice of covariance/correlation for Y-axis on C-plot

label_features <- my_env$labelFeatures
labelfeatures_check <- TRUE
if ( is.na(label_features) ) {
  labelfeatures_check <- FALSE

  # receiver for result of the call to corcov_calc
  my_result <- NULL

  # compute and plot the correlation_vs_covariance details plot
  #   The parameter settings here are generally taken from bioconductor ropls::plot.opls source.
  if ( my_env$cplot_p || my_env$cplot_o ) {
    old_par <- par(
      font        = 2         # bold font face
    , font.axis   = 2         # bold font face for axis
    , font.lab    = 2         # bold font face for x and y labels
    , lwd         = 2         # line-width - interpretation is device spcific
    , pch         = 18        # black diamond plot-character, see help for graphics::points
    , pty         = "m"       # do not force plots to be square
    , no.readonly = TRUE      # only save writable parameters
    )
    pdf_height <- 12
    pdf_width  <- 8
    my_layout <- function() {
      # lay out 2 columns by 3 rows with extra width at the margin of individual plots
      layout(
        matrix(
          # blank row  plot 1 & 2  blank row  plot 3 & 4  blank row  plot 5 & 6 blank row
          c(0,0,0,0,0, 0,1,0,2,0,  0,0,0,0,0, 0,3,0,4,0,  0,0,0,0,0, 0,5,0,6,0, 0,0,0,0,0)
        , nrow = 7
        , ncol = 5
        , byrow = TRUE
        )
        # slim columns 1, 3, and 5
      , widths  = c(0.1, 0.9, 0.1, 0.9, 0.1)
        # slim rows 1, 3, 5, and 7
      , heights = c(0.1, 0.9, 0.1, 0.9, 0.1, 0.9, 0.1)
      )
    }
  } else {
    old_par <- par(
      font        = 2         # bold font face
    , font.axis   = 2         # bold font face for axis
    , font.lab    = 2         # bold font face for x and y labels
    , lwd         = 2         # line-width - interpretation is device spcific
    , pch         = 18        # black diamond plot-character, see help for graphics::points
    , pty         = "m"       # do not force plots to be square
    , no.readonly = TRUE      # only save writable parameters
    )
    pdf_height <- 8
    pdf_width  <- 8
    my_layout <- function() {
      # lay out 2 columns by 2 rows with extra width at the margin of individual plots
      layout(
        matrix(
          # blank row  plot 1 & 2  blank row  plot 3 & 4  blank row
          c(0,0,0,0,0, 0,1,0,2,0,  0,0,0,0,0, 0,3,0,4,0,  0,0,0,0,0)
        , nrow = 5
        , ncol = 5
        , byrow = TRUE
        )
        # slim columns 1, 3, and 5
      , widths  = c(0.1, 0.9, 0.1, 0.9, 0.1)
        # slim rows 1, 3, and 5
      , heights = c(0.1, 0.9, 0.1, 0.9, 0.1)
      )
    }
  }
  plot2pdf(
    file.name = my_env$contrast_detail
  , width  = pdf_width
  , height = pdf_height
  , plot.function = function() {
      # plot layout four or six plots per page
      my_layout()
      my_result <<- corcov_calc(
          calc_env            = my_env
        , failure_action      = my_fatal
        , progress_action     = my_log
        , corcov_tsv_action   = corcov_tsv_action
        , salience_tsv_action = salience_tsv_action
        )
    }
  )
  par(old_par)

  my_log( "--------------------------  Finished data processing  --------------------------")
}

my_log( "End of the '", modNamC, "' Galaxy module call")