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bin2d.R
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#!/bin/env Rscript
args <- commandArgs()
scriptPath = strsplit(args[4], '=', fixed = T)[[1]][2]
scriptName = basename(scriptPath)
scriptDir = dirname(scriptPath)
args = args[-(1:5)]
source(paste0(scriptDir, '/common.R'))
usage = function(){
cat(paste0("Usage: ", scriptName) )
cat(" -p=outputName.pdf <input.tsv
Option:
-p|pdf FILE The output figure in pdf[figure.pdf]
-w|width INT The figure width
-m|main STR The main title
-mainS DOU The size of main title[20 for ggplot]
-x|xlab STR The xlab
-y|ylab STR The ylab
-xl|xlog INT Transform the X scale to INT base log
-yl|ylog INT Transform the Y scale to INT base log
-x1 INT The xlim start
-x2 INT The xlim end
-y1 INT The ylim start
-y2 INT The ylim end
-h|help Show help
-b|bin DOU The bin number on X and Y
-binWidthX DOU The bin width on X
-binWidthY DOU The bin width on Y
-a|alpha DOU The alpha of cell body
-alphaV STR The column name to apply alpha (V3, V4, ...)
-alphaT STR The title of alpha legend[Alpha]
-alphaTP POS The title position of alpha legend[horizontal: top, vertical:right]
-alphaLP POS The label position of alpha legend[horizontal: top, vertical:right]
-alphaD STR The direction of alpha legend (horizontal, vertical)
-c|color STR The color of cell boundary
-colorV STR The column name to apply color (V3, V4,...)
-colorC Continuous color mapping
-colorT STR The title of color legend[Color]
-colorTP POS The title position of color legend[horizontal: top, vertical:right]
-colorLP POS The label position of color legend[horizontal: top, vertical:right]
-colorD STR The direction of color legend (horizontal, vertical)
-f|fill STR The color of cell body
-fillV STR The column name to apply fill (V3, V4,...)
-fillT STR The title of fill legend[Fill]
-fillTP POS The title position of fill legend[horizontal: top, vertical:right]
-fillLP POS The label position of fill legend[horizontal: top, vertical:right]
-fillD STR The direction of fill legend (horizontal, vertical)
-l|linetype INT The line type
-linetypeV STR The column name to apply linetype (V3, V4,...)
-linetypeT STR The title of linetype legend[Line Type]
-linetypeTP POS The title position of linetype legend[horizontal: top, vertical:right]
-linetypeLP POS The label position of linetype legend[horizontal: top, vertical:right]
-linetypeD STR The direction of linetype legend (horizontal, vertical)
-s|size DOU The size of cell body
-sizeV STR The column name to apply size (V3, V4,...)
-sizeT STR The title of size legend[Size]
-sizeTP POS The title position of size legend[horizontal: top, vertical:right]
-sizeLP POS The label position of size legend[horizontal: top, vertical:right]
-sizeD STR The direction of size legend (horizontal, vertical)
-weight DOU The weight of box
-weightV STR The column name to apply weight (V3, V4,...)
-weightT STR The title of weight legend[weight]
-weightTP POS The title position of weight legend[horizontal: top, vertical:right]
-weightLP POS The label position of weight legend[horizontal: top, vertical:right]
-weightD STR The direction of weight legend (horizontal, vertical)
-noGuide Don't show the legend guide
-lgPos POS The legend position[horizontal: top, vertical:right]
-lgPosX [0,1] The legend relative postion on X
-lgPosY [0,1] The legend relative postion on Y
-lgTtlS INT The legend title size[15]
-lgTxtS INT The legend text size[15]
-lgBox STR The legend box style (horizontal, vertical)
-fp|flip Flip the Y axis to horizontal
-facet STR The facet type (facet_wrap, facet_grid)
-facetM STR The facet model (eg: '. ~ V3', 'V3 ~ .', 'V3 ~ V4', '. ~ V3 + V4', ...)
-facetScl STR The axis scale in each facet ([fixed], free, free_x or free_y)
-xPer Show X label in percentage
-yPer Show Y label in percentage
-xComma Show X label number with comma seperator
-yComma Show Y label number with comma seperator
-axisRatio DOU The fixed aspect ratio between y and x units
-annoTxt STRs The comma-seperated texts to be annotated
-annoTxtX INTs The comma-seperated X positions of text
-annoTxtY INTs The comma-seperated Y positions of text
Skill:
Legend title of alpha, color, etc can be set as the same to merge their guides
")
q(save = 'no')
}
alphaT = 'Alpha'
colorT = 'Color'
fillT = 'Fill'
linetypeT = 'Line Type'
sizeT = 'Size'
weightT = 'Weight'
lgTtlS = 15
lgTxtS = 15
showGuide = TRUE
myPdf = 'figure.pdf'
mainS = 20
if(length(args) >= 1){
for(i in 1:length(args)){
arg = args[i]
tmp = parseArgAsNum(arg, 'b(in)?', 'bin'); if(!is.null(tmp)) bin = tmp
tmp = parseArgAsNum(arg, 'binWidthX', 'binWidthX'); if(!is.null(tmp)) binWidthX = tmp
tmp = parseArgAsNum(arg, 'binWidthY', 'binWidthY'); if(!is.null(tmp)) binWidthY = tmp
tmp = parseArgAsNum(arg, 'a(lpha)?', 'a'); if(!is.null(tmp)) alpha = tmp
tmp = parseArg(arg, 'alphaV', 'alphaV'); if(!is.null(tmp)) alphaV = tmp
tmp = parseArg(arg, 'alphaT', 'alphaT'); if(!is.null(tmp)) alphaT = tmp
tmp = parseArg(arg, 'alphaTP', 'alphaTP'); if(!is.null(tmp)) alphaTP = tmp
tmp = parseArg(arg, 'alphaLP', 'alphaLP'); if(!is.null(tmp)) alphaLP = tmp
tmp = parseArg(arg, 'alphaD', 'alphaD'); if(!is.null(tmp)) alphaD = tmp
tmp = parseArg(arg, 'c(olor)?', 'c'); if(!is.null(tmp)) color = tmp
tmp = parseArg(arg, 'colorV', 'colorV'); if(!is.null(tmp)) colorV = tmp
if(arg == '-colorC') colorC = TRUE
tmp = parseArg(arg, 'colorT', 'colorT'); if(!is.null(tmp)) colorT = tmp
tmp = parseArg(arg, 'colorTP', 'colorTP'); if(!is.null(tmp)) colorTP = tmp
tmp = parseArg(arg, 'colorLP', 'colorLP'); if(!is.null(tmp)) colorLP = tmp
tmp = parseArg(arg, 'colorD', 'colorD'); if(!is.null(tmp)) colorD = tmp
tmp = parseArgAsNum(arg, 'f(ill)?', 'l'); if(!is.null(tmp)) fill = tmp
tmp = parseArg(arg, 'f(ill)?', 'f'); if(!is.null(tmp)) fill = tmp
tmp = parseArg(arg, 'fillV', 'fillV'); if(!is.null(tmp)) fillV = tmp
tmp = parseArg(arg, 'fillT', 'fillT'); if(!is.null(tmp)) fillT = tmp
tmp = parseArg(arg, 'fillTP', 'fillTP'); if(!is.null(tmp)) fillTP = tmp
tmp = parseArg(arg, 'fillLP', 'fillLP'); if(!is.null(tmp)) fillLP = tmp
tmp = parseArg(arg, 'fillD', 'fillD'); if(!is.null(tmp)) fillD = tmp
tmp = parseArgAsNum(arg, 'l(inetype)?', 'l'); if(!is.null(tmp)) linetype = tmp
tmp = parseArg(arg, 'linetypeV', 'linetypeV'); if(!is.null(tmp)) linetypeV = tmp
tmp = parseArg(arg, 'linetypeT', 'linetypeT'); if(!is.null(tmp)) linetypeT = tmp
tmp = parseArg(arg, 'linetypeTP', 'linetypeTP'); if(!is.null(tmp)) linetypeTP = tmp
tmp = parseArg(arg, 'linetypeLP', 'linetypeLP'); if(!is.null(tmp)) linetypeLP = tmp
tmp = parseArg(arg, 'linetypeD', 'linetypeD'); if(!is.null(tmp)) linetypeD = tmp
tmp = parseArgAsNum(arg, 's(ize)?', 's'); if(!is.null(tmp)) size = tmp
tmp = parseArg(arg, 'sizeV', 'sizeV'); if(!is.null(tmp)) sizeV = tmp
tmp = parseArg(arg, 'sizeT', 'sizeT'); if(!is.null(tmp)) sizeT = tmp
tmp = parseArg(arg, 'sizeTP', 'sizeTP'); if(!is.null(tmp)) sizeTP = tmp
tmp = parseArg(arg, 'sizeLP', 'sizeLP'); if(!is.null(tmp)) sizeLP = tmp
tmp = parseArg(arg, 'sizeD', 'sizeD'); if(!is.null(tmp)) sizeD = tmp
tmp = parseArgAsNum(arg, 'weight', 'weight'); if(!is.null(tmp)) weight = tmp
tmp = parseArg(arg, 'weightV', 'weightV'); if(!is.null(tmp)) weightV = tmp
tmp = parseArg(arg, 'weightT', 'weightT'); if(!is.null(tmp)) weightT = tmp
tmp = parseArg(arg, 'weightTP', 'weightTP'); if(!is.null(tmp)) weightTP = tmp
tmp = parseArg(arg, 'weightLP', 'weightLP'); if(!is.null(tmp)) weightLP = tmp
tmp = parseArg(arg, 'weightD', 'weightD'); if(!is.null(tmp)) weightD = tmp
if(arg == '-noGuide') showGuide = FALSE
tmp = parseArg(arg, 'lgPos', 'lgPos'); if(!is.null(tmp)) lgPos = tmp
tmp = parseArgAsNum(arg, 'lgPosX', 'lgPosX'); if(!is.null(tmp)) lgPosX = tmp
tmp = parseArgAsNum(arg, 'lgPosY', 'lgPosY'); if(!is.null(tmp)) lgPosY = tmp
tmp = parseArgAsNum(arg, 'lgTtlS', 'lgTtlS'); if(!is.null(tmp)) lgTtlS = tmp
tmp = parseArgAsNum(arg, 'lgTxtS', 'lgTxtS'); if(!is.null(tmp)) lgTxtS = tmp
tmp = parseArg(arg, 'lgBox', 'lgBox'); if(!is.null(tmp)) lgBox = tmp
if(arg == '-fp' || arg =='-flip') flip = TRUE
tmp = parseArg(arg, 'facet', 'facet'); if(!is.null(tmp)) myFacet = tmp
tmp = parseArg(arg, 'facetM', 'facetM'); if(!is.null(tmp)) facetM = tmp
tmp = parseArg(arg, 'facetScl', 'facetScl'); if(!is.null(tmp)) facetScl = tmp
if(arg == '-xPer') xPer = TRUE
if(arg == '-yPer') yPer = TRUE
if(arg == '-xComma') xComma = TRUE
if(arg == '-yComma') yComma = TRUE
tmp = parseArgAsNum(arg, 'axisRatio', 'axisRatio'); if(!is.null(tmp)) axisRatio = tmp
tmp = parseArg(arg, 'annoTxt', 'annoTxt'); if(!is.null(tmp)) annoTxt = tmp
tmp = parseArg(arg, 'annoTxtX', 'annoTxtX'); if(!is.null(tmp)) annoTxtX = tmp
tmp = parseArg(arg, 'annoTxtY', 'annoTxtY'); if(!is.null(tmp)) annoTxtY = tmp
if(arg == '-h' || arg == '-help') usage()
tmp = parseArg(arg, 'p(df)?', 'p'); if(!is.null(tmp)) myPdf = tmp
tmp = parseArgAsNum(arg, 'w(idth)?', 'w'); if(!is.null(tmp)) width = tmp
tmp = parseArgAsNum(arg, 'x1', 'x1'); if(!is.null(tmp)) x1 = tmp
tmp = parseArgAsNum(arg, 'x2', 'x2'); if(!is.null(tmp)) x2 = tmp
tmp = parseArgAsNum(arg, 'y1', 'y1'); if(!is.null(tmp)) y1 = tmp
tmp = parseArgAsNum(arg, 'y2', 'y2'); if(!is.null(tmp)) y2 = tmp
tmp = parseArgAsNum(arg, 'xl(og)?', 'xl'); if(!is.null(tmp)) xLog = tmp
tmp = parseArgAsNum(arg, 'yl(og)?', 'yl'); if(!is.null(tmp)) yLog = tmp
tmp = parseArg(arg, 'm(ain)?', 'm'); if(!is.null(tmp)) main = tmp
tmp = parseArgAsNum(arg, 'mainS', 'mainS'); if(!is.null(tmp)) mainS = tmp
tmp = parseArg(arg, 'x(lab)?', 'x'); if(!is.null(tmp)) xLab = tmp
tmp = parseArg(arg, 'y(lab)?', 'y'); if(!is.null(tmp)) yLab = tmp
}
}
if(exists('width')){
pdf(myPdf, width = width)
}else{
pdf(myPdf)
}
data = read.delim(file('stdin'), header = F)
library(ggplot2)
p = ggplot(data, aes(x = V1, y = V2))
if(exists('alphaV')){
p = p + aes_string(alpha = alphaV)
myCmd = 'p = p + guides(alpha = guide_legend(alphaT'
if(exists('alphaTP')) myCmd = paste0(myCmd, ', title.position = alphaTP')
if(exists('alphaLP')) myCmd = paste0(myCmd, ', label.position = alphaLP')
if(exists('alphaD')) myCmd = paste0(myCmd, ', direction = alphaD')
myCmd = paste0(myCmd, '))')
eval(parse(text = myCmd))
}
if(exists('colorV')){
if(exists('colorC')){
p = p + aes_string(color = colorV)
}else{
myCmd = paste0('p = p + aes(color = factor(', colorV, '))'); eval(parse(text = myCmd))
}
myCmd = 'p = p + guides(color = guide_legend(colorT'
if(exists('colorTP')) myCmd = paste0(myCmd, ', title.position = colorTP')
if(exists('colorLP')) myCmd = paste0(myCmd, ', label.position = colorLP')
if(exists('colorD')) myCmd = paste0(myCmd, ', direction = colorD')
myCmd = paste0(myCmd, '))')
eval(parse(text = myCmd))
}
if(exists('fillV')){
myCmd = paste0('p = p + aes(fill = ', fillV, ')'); eval(parse(text = myCmd))
myCmd = 'p = p + guides(fill = guide_legend(fillT'
if(exists('fillTP')) myCmd = paste0(myCmd, ', title.position = fillTP')
if(exists('fillLP')) myCmd = paste0(myCmd, ', label.position = fillLP')
if(exists('fillD')) myCmd = paste0(myCmd, ', direction = fillD')
myCmd = paste0(myCmd, '))')
eval(parse(text = myCmd))
}
if(exists('linetypeV')){
myCmd = paste0('p = p + aes(linetype = factor(', linetypeV, '))'); eval(parse(text = myCmd))
myCmd = 'p = p + guides(linetype = guide_legend(linetypeT'
if(exists('linetypeTP')) myCmd = paste0(myCmd, ', title.position = linetypeTP')
if(exists('linetypeLP')) myCmd = paste0(myCmd, ', label.position = linetypeLP')
if(exists('linetypeD')) myCmd = paste0(myCmd, ', direction = linetypeD')
myCmd = paste0(myCmd, '))')
eval(parse(text = myCmd))
}
if(exists('sizeV')){
p = p + aes_string(size = sizeV)
myCmd = 'p = p + guides(size = guide_legend(sizeT'
if(exists('sizeTP')) myCmd = paste0(myCmd, ', title.position = sizeTP')
if(exists('sizeLP')) myCmd = paste0(myCmd, ', label.position = sizeLP')
if(exists('sizeD')) myCmd = paste0(myCmd, ', direction = sizeD')
myCmd = paste0(myCmd, '))')
eval(parse(text = myCmd))
}
if(exists('weightV')){
p = p + aes_string(weight = weightV)
myCmd = 'p = p + guides(weight = guide_legend(weightT'
if(exists('weightTP')) myCmd = paste0(myCmd, ', title.position = weightTP')
if(exists('weightLP')) myCmd = paste0(myCmd, ', label.position = weightLP')
if(exists('weightD')) myCmd = paste0(myCmd, ', direction = weightD')
myCmd = paste0(myCmd, '))')
eval(parse(text = myCmd))
}
myCmd = 'p = p + geom_bin2d(show_guide = showGuide, '
if(exists('bin')) myCmd = paste0(myCmd, ', bins = bin')
if(exists("binWidthX") && exists("binWidthY")) myCmd = paste0(myCmd, ', binwidth = c(binWidthX, binWidthY)')
if(exists('alpha')) myCmd = paste0(myCmd, ', alpha = alpha')
if(exists('color')) myCmd = paste0(myCmd, ', color = color')
if(exists('fill')) myCmd = paste0(myCmd, ', fill = fill')
if(exists('size')) myCmd = paste0(myCmd, ', size = size')
myCmd = paste0(myCmd, ')')
eval(parse(text = myCmd))
if(exists('myFacet')){
myCmd = paste0('p = p + ', myFacet, '("' + facetM + '"')
if(exists('facetScl')) myCmd = paste0(myCmd, ', scale = facetScl')
myCmd = paste0(myCmd, ')')
eval(parse(text = myCmd))
}
if(exists('lgPos')) p = p + theme(legend.position = lgPos)
if(exists('lgPosX') && exists('lgPosY')) p = p + theme(legend.position = c(lgPosX, lgPosY))
p = p + theme(legend.title = element_text(size = lgTtlS), legend.text = element_text(size = lgTxtS))
if(exists('lgBox')) p = p + theme(legend.box = lgBox)
if(exists('xPer')) p = p + scale_x_continuous(labels = percent)
if(exists('yPer')) p = p + scale_y_continuous(labels = percent)
if(exists('xComma')) p = p + scale_x_continuous(labels = comma)
if(exists('yComma')) p = p + scale_y_continuous(labels = comma)
if(exists('axisRatio')) p = p + coord_fixed(ratio = axisRatio)
if(exists('annoTxt')) p = p + annotate('text', x = as.numeric(strsplit(annoTxtX, ',', fixed = T)),
y = as.numeric(strsplit(annoTxtY, ',', fixed = T)),
label = strsplit(annoTxt, ',', fixed = T))
if(exists('x1') && exists('x2')) p = p + coord_cartesian(xlim = c(x1, x2))
if(exists('y1') && exists('y2')) p = p + coord_cartesian(ylim = c(y1, y2))
if(exists('x1') && exists('x2') && exists('y1') && exists('y2')) p = p + coord_cartesian(xlim = c(x1, x2), ylim = c(y1, y2))
if(exists('xLog') || exists('yLog')){
library(scales)
if(exists('xLog')) p = p + scale_x_continuous(trans = log_trans(xLog))
if(exists('yLog')) p = p + scale_y_continuous(trans = log_trans(yLog))
p = p + annotation_logticks() + theme(panel.grid.minor = element_blank())
}
if(exists('main')) p = p + ggtitle(main)
p = p + theme(plot.title = element_text(size = mainS))
if(exists('xLab')) p = p + xlab(xLab) + theme(axis.title.x = element_text(size = mainS*0.8), axis.text.x = element_text(size = mainS*0.7))
if(exists('yLab')) p = p + ylab(yLab)
p = p + theme(axis.title.y = element_text(size = mainS*0.8), axis.text.y = element_text(size = mainS*0.7))
if(exists('horizontal')) p = p + geom_hline(yintercept = horizontal, linetype = "longdash", size = 0.3)
p