getcolors <- function(cols, n) {
  if (n > length(cols)) {
    cols <- c(cols, adjustcolor(cols, alpha.f=0.8))
  }
  return(cols[1:n])
}

remove__ <- function(s, patten='__') {
  if (grepl(patten, s)) {
    s <- strsplit(s, patten)[[1]][2]
  }
  return(s)
}

select <- function(data, abundance=0, topnum=0, firstnum=0, minsample=0, sort=1, unclass=TRUE, merge=FALSE, other=TRUE, per=TRUE, remove=TRUE) {
  data <- data[rowSums(data) > 0, , drop=F]
  if (nrow(data) == 1) {
    if (per) {data[1,] <- 100}
    return(data)
  }
  if (max(data) > 100) {
    abu <- apply(data, 2, function(x) x/sum(x)*100)
  } else {
    abu <- data
  }
  
  II <- rep(0, nrow(abu))
  if (abundance != 0) {
    for (i in 1:nrow(abu)) {
      if (max((abu[i,]) > abundance)){
        II[i] <- 1
      }
    }
  } else if (topnum != 0) {
    rowSum <- rowSums(abu)
    index <- rev(order(rowSum))
    if (nrow(abu) > topnum) {
      II[index[1:topnum]] <- 1
    } else {
      II <- rep(1, nrow(abu))
    }
  } else if (firstnum != 0) {
    for (i in 1:ncol(abu)) {
      index <- rev(order(abu[, i]))
      if (nrow(abu) > firstnum) {
        II[index[1:firstnum]] <- 1
      } else {
        II <- rep(1, nrow(abu))
      }
    }
  } else if (minsample != 0) {
    count <- ifelse(minsample > 1, minsample, minsample*ncol(abu))
    for (i in 1:nrow(abu)) {
      if (length(which(abu[1,]>0)) > minsample){
        II[i] <- 1
      }
    }
  } else {
    II <- rep(1, nrow(abu))
  }
  
  selectabu <- abu[which(II==1), , drop=F]
  
  if (sort != 0) {
    rowSum <- rowSums(selectabu)
    index <- order(rowSum)
    if (sort == 1) {
      selectabu <- selectabu[rev(index), , drop=F]
    } else {
      selectabu <- selectabu[index, , drop=F]
    }
  }
  
  selectdata <- data[rownames(selectabu), , drop=F]
  usedata <- selectdata
  
  if (unclass) {
    unclass <- sapply(rownames(selectdata), function(x) grepl('unclassified', x, perl=T))
    unclassdata <- selectdata[unclass, , drop=F]
    classdata <- selectdata[!unclass, , drop=F]
    
    if (sum(unclass) > 0) {
      if (merge) {
        Unclassified <- colSums(unclassdata)
        Unclassified <- t(data.frame(Unclassified))
        usedata <- rbind(classdata, Unclassified)
      } else {
        usedata <- rbind(classdata, unclassdata)
      }
    }
  }
  
  resdata <- usedata
  if (other) {
    if (length(which(II==0)) > 1) {
      Other <- colSums(data[which(II==0), , drop=F])
      Other <- t(data.frame(Other))
      resdata <- rbind(usedata, Other)
    } else if (length(which(II==0)) == 1) {
      resdata <- rbind(usedata, data[which(II==0), , drop=F])
    }
  }
  if (per & (max(data) > 100)) {
    if (nrow(resdata) > 1) {
      #resdata <- apply(resdata, 2, function(x) x/sum(x)*100)
      resdata <- t(t(resdata) / colSums(data) * 100)
    } else {
      resdata[1,] <- 100
    }
  }
  
  if (remove){
    rownames(resdata) <- sapply(rownames(resdata), remove__)
  }
  
  return(resdata)
}




data <- read.table('genus_count.xls', header=T, sep='\t', check.names=F, row.names=1)
name <- 'genus' 

palette <- c('#CA0000','#0087FF','#00BA1D','#CF00FF','#00DBE2','#FFAF00','#0017F4','#006012','#6F1A1A','#B5CF00','#009E73','#F0E442','#D55E00','#CC79A7','#FF8A8A','#AA6400','#50008A','#00FF58','#E175FF','#FFCC99','#009999','#CC0066','#C0C0C0','#666600','#505050','#56B4E9','#0072B2','#33FF33','#99004c','#CCFF99','#660066','#9370DB','#D8BFD8','#BC8F8F','#2F4F4F','#FF6347','#877878','#CD5C5C','#FF0000','#00FF00','#000080','#0D7339','#3D90D9','#D98236','#DF514F','#8CCDA3','#F5E2D7','#FACBBE','#EA4885','#E69F00')  #sangon 默认配色

abundance <- 1
topnum <- 0 
firstnum <- 0 
minsample <- 0 

sort <- 1 
unclass <- TRUE 
merge <- FALSE 
other <- TRUE 
per <- TRUE 
remove <- TRUE 

xlab <- '' 
ylab <- 'Relative Abundance (%)' 
title <- '' 

plotdata <- select(data, abundance, topnum, firstnum, minsample, sort, unclass, merge, other, per, remove)
write.table(plotdata, paste0(name, '.xls'), sep='\t', col.names=NA, quote=F)
left <- ceiling(ncol(plotdata)/10) + 2
right <- ceiling(nrow(plotdata)/30)
right <- ifelse(max(nchar(rownames(plotdata)))>10, 2*right, 1.2*right)
layout(matrix(c(1, 2), 1), c(left, right))
par(mar=c(4, 3, 2, 0), mgp=c(1.7, 0.7, 0))

if ('Other' %in% rownames(plotdata)) {
  cols <- c(getcolors(palette, nrow(plotdata)-1), 'grey')
} else {
  cols <- getcolors(palette, nrow(plotdata))
}
bar <- barplot(as.matrix(plotdata), xlab=xlab, ylab=ylab, xaxt='n', yaxt='n', col=cols, cex.lab=1, main=title)
text(bar, par('usr')[3], labels=colnames(plotdata), cex=ifelse(ncol(plotdata)>30,0.6,0.8), srt=45, adj=c(1, 1), xpd=NA)
axis(2, las=2, cex.axis=.8)
par(mar=c(1, 1, 1, 0))
plot.new()
legend('left', col=cols, legend=rownames(plotdata), pch=15, bty='n', cex=.6, text.font=3, ncol=ceiling(nrow(plotdata)/40))