-
Notifications
You must be signed in to change notification settings - Fork 2
/
Copy pathdensity2D.R
executable file
·278 lines (254 loc) · 14.2 KB
/
density2D.R
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
#!/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:
Common:
-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
-ng|noGgplot Draw figure in the style of R base rather than ggplot
-h|help Show help
ggplot specific:
-geom STR The geometric object to use display the data ([density2d], tile, point, polygon)
-noContour Do not contour the results of the 2d density estimation
-n INT Number of grid points in each direction
-a|alpha DOU The alpha of contour
-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 contour
-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)
-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 contour 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)
-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'
linetypeT = 'Line Type'
sizeT = 'Size'
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 = parseArg(arg, 'geom', 'geom'); if(!is.null(tmp)) geom = tmp
tmp = parseArgAsNum(arg, 'n', 'n'); if(!is.null(tmp)) n = tmp
if(arg == '-noContour') noContour = TRUE
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, '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
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
if(arg == '-ng' || arg == '-noGgplot') noGgplot = TRUE
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))
myCmd = 'p = p + stat_density2d(show_guide = showGuide, '
if(exists('bin')) myCmd = paste0(myCmd, ', bins = bin')
if(exists('binWidth')) myCmd = paste0(myCmd, ', binwidth = binWidth')
if(exists('geom')) myCmd = paste0(myCmd, ', geom = geom')
if(exists('alpha')) myCmd = paste0(myCmd, ', alpha = alpha')
if(exists('color')) myCmd = paste0(myCmd, ', color = color')
if(exists('size')) myCmd = paste0(myCmd, ', size = size')
if(exists('noContour')) myCmd = paste0(myCmd, ', contour = F')
myCmd = paste0(myCmd, ')')
eval(parse(text = myCmd))
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('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))
}
if(exists('myFacet')){
myCmd = '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))
p