R/01_utils.R

In exaexa/ShinySOM: Shiny-based DiffSOM workflow wrapper

persistentP <- function(input, id, default) {
  isolate(if(is.null(input[[id]])) default else input[[id]])
}

findColIds <- function(cols, all) {
  seq_len(length(all))[all %in% cols]
}

namesInvert <- function(c) {
  r <- names(c)
  names(r) <- c
  r
}

ilDiv <- function(..., style='') div(
  style=paste0('display: inline-block;', style), ...)

sliderPointSize <- function(id, value=0) tooltip("Extra point radius in the scatterplot, in pixels. 0 = only a single pixel for each cell.",
  sliderInput(id, "Extra point size", value=value, min=0, max=3, step=.1))

sliderAlpha <- function(id, value=0.3) tooltip("Transparency of cells in the scatterplot.",
  sliderInput(id, "Alpha", value=value, min=0.01, max=1, step=.01))

setClustNAs <- function(x) {
  x[x==' ']<-NA
  x
}

unsetClustNAs <- function(x) {
  x[is.na(x)] <- ' '
  x
}

getHeatmapColors <- function(ds, colors) {
  if(is.null(colors)) return(NULL)
  ids <- findColIds(colors, ds$colsToUse)
  if(length(ids)==0) return(NULL)

  pal <- EmbedSOM::ExpressionPalette(100)
  d <- apply(ds$map$codes[,ids,drop=F], 2,
    function(col) pal[1+as.integer(99*EmbedSOM::NormalizeColor(col))])
  colnames(d) <- ds$colsToUse[ids]
  d
}

plotClusterTextAnnotation <- function(e, cl, annotation, centerFunction=median, ...) {
  if(is.null(cl)) return()
  if(is.null(annotation)) return()

  if(!is.factor(cl)) cl <- factor(cl)

  centers <- t(sapply(levels(cl),
    function(x)
      apply(e[!is.na(cl) & cl==x,], 2, centerFunction)
  ))

  if(nlevels(cl)>0)
    text(centers, annotation[levels(cl)], ...)
}

pad.zero <- function(v, l) {
  if(length(v)==l) {
    v
  } else if (length(v)>l) {
    v[1:l]
  }  else {
    c(v, rep(0, times=l-length(v)))
  }
}