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专业背景:计算机科学 研究方向与兴趣: JavaEE-Web软件开发, 生物信息学, 数据挖掘与机器学习, 智能信息系统 目前工作: 基因组, 转录组, NGS高通量数据分析, 生物数据挖掘, 植物系统发育和比较进化基因组学

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R 的颜色设置与包及MAplot及scatterplots图  

2010-10-18 20:35:54|  分类: R&Bioconductor |  标签: |举报 |字号 订阅

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 Bioinformatics and Computational Biology Solutions Using R and Bioconductor 第三章

 

> library("affy")
> library("ALLMLL")
> data(MLL.B)
> Data <- MLL.B[, c(2, 1, 3:5, 14, 6, 13)]
> sampleNames(Data) <- letters[1:8]

> library("RColorBrewer")
> cols <- brewer.pal(8, "Set1")
> boxplot(Data, col = cols)
The RColorBrewer package is used to select a nice color palette

> hist(Data, col = cols, lty = 1, xlab = "Log (base 2) intensities")
> legend(12, 1, letters[1:8], lty = 1, col = cols)

 

A loess curve is fitted to the scatter-plot to summarize any nonlinear
relationship. Since there are only 8 arrays in this data set, MA-plots
for all 8 can be examined using the following code.
> par(mfrow = c(2, 4))
> MAplot(Data, cex = 0.75)
> mtext("M", 2, outer = TRUE)
> mtext("A", 1, outer = TRUE)

 

 

另外,颜色的设置还有:

> col=palette() #默认
> col
[1] "black"   "red"     "green3"  "blue"    "cyan"    "magenta" "yellow"
[8] "gray"  
> col1=rainbow()
错误于rainbow() : 缺少变元"n",也没有缺省值
> col1=rainbow(20)
> col1
 [1] "#FF0000FF" "#FF4C00FF" "#FF9900FF" "#FFE500FF" "#CCFF00FF" "#80FF00FF"
 [7] "#33FF00FF" "#00FF19FF" "#00FF66FF" "#00FFB2FF" "#00FFFFFF" "#00B3FFFF"
[13] "#0066FFFF" "#0019FFFF" "#3300FFFF" "#8000FFFF" "#CC00FFFF" "#FF00E6FF"
[19] "#FF0099FF" "#FF004DFF"
> col2=colors()
> col2
  [1] "white"                "aliceblue"            "antiquewhite"       
  [4] "antiquewhite1"        "antiquewhite2"        "antiquewhite3"      
  [7] "antiquewhite4"        "aquamarine"           "aquamarine1"        
 [10] "aquamarine2"          "aquamarine3"          "aquamarine4"        
 [13] "azure"                "azure1"               "azure2"             
 [16] "azure3"               "azure4"               "beige"              
 [19] "bisque"               "bisque1"              "bisque2"            
 [22] "bisque3"              "bisque4"              "black"              
 [25] "blanchedalmond"       "blue"                 "blue1"              
 [28] "blue2"                "blue3"                "blue4"              
 [31] "blueviolet"           "brown"                "brown1"             
 [34] "brown2"               "brown3"               "brown4"             
 [37] "burlywood"            "burlywood1"           "burlywood2"         
 [40] "burlywood3"           "burlywood4"           "cadetblue"          
 [43] "cadetblue1"           "cadetblue2"           "cadetblue3"         
 [46] "cadetblue4"           "chartreuse"           "chartreuse1"        
 [49] "chartreuse2"          "chartreuse3"          "chartreuse4"        
 [52] "chocolate"            "chocolate1"           "chocolate2"         
 [55] "chocolate3"           "chocolate4"           "coral"              
 [58] "coral1"               "coral2"               "coral3"             
 [61] "coral4"               "cornflowerblue"       "cornsilk"           
 [64] "cornsilk1"            "cornsilk2"            "cornsilk3"          
 [67] "cornsilk4"            "cyan"                 "cyan1"              
 [70] "cyan2"                "cyan3"                "cyan4"              
 [73] "darkblue"             "darkcyan"             "darkgoldenrod"      
 [76] "darkgoldenrod1"       "darkgoldenrod2"       "darkgoldenrod3"     
 [79] "darkgoldenrod4"       "darkgray"             "darkgreen"          
 [82] "darkgrey"             "darkkhaki"            "darkmagenta"        
 [85] "darkolivegreen"       "darkolivegreen1"      "darkolivegreen2"    
 [88] "darkolivegreen3"      "darkolivegreen4"      "darkorange"         
 [91] "darkorange1"          "darkorange2"          "darkorange3"        
 [94] "darkorange4"          "darkorchid"           "darkorchid1"        
 [97] "darkorchid2"          "darkorchid3"          "darkorchid4"        
[100] "darkred"              "darksalmon"           "darkseagreen"       
[103] "darkseagreen1"        "darkseagreen2"        "darkseagreen3"      
[106] "darkseagreen4"        "darkslateblue"        "darkslategray"      
[109] "darkslategray1"       "darkslategray2"       "darkslategray3"     
[112] "darkslategray4"       "darkslategrey"        "darkturquoise"      
[115] "darkviolet"           "deeppink"             "deeppink1"          
[118] "deeppink2"            "deeppink3"            "deeppink4"          
[121] "deepskyblue"          "deepskyblue1"         "deepskyblue2"       
[124] "deepskyblue3"         "deepskyblue4"         "dimgray"            
[127] "dimgrey"              "dodgerblue"           "dodgerblue1"        
[130] "dodgerblue2"          "dodgerblue3"          "dodgerblue4"        
[133] "firebrick"            "firebrick1"           "firebrick2"         
[136] "firebrick3"           "firebrick4"           "floralwhite"        
[139] "forestgreen"          "gainsboro"            "ghostwhite"         
[142] "gold"                 "gold1"                "gold2"              
[145] "gold3"                "gold4"                "goldenrod"          
[148] "goldenrod1"           "goldenrod2"           "goldenrod3"         
[151] "goldenrod4"           "gray"                 "gray0"              
[154] "gray1"                "gray2"                "gray3"              
[157] "gray4"                "gray5"                "gray6"              
[160] "gray7"                "gray8"                "gray9"              
[163] "gray10"               "gray11"               "gray12"             
[166] "gray13"               "gray14"               "gray15"             
[169] "gray16"               "gray17"               "gray18"             
[172] "gray19"               "gray20"               "gray21"             
[175] "gray22"               "gray23"               "gray24"             
[178] "gray25"               "gray26"               "gray27"             
[181] "gray28"               "gray29"               "gray30"             
[184] "gray31"               "gray32"               "gray33"             
[187] "gray34"               "gray35"               "gray36"             
[190] "gray37"               "gray38"               "gray39"             
[193] "gray40"               "gray41"               "gray42"             
[196] "gray43"               "gray44"               "gray45"             
[199] "gray46"               "gray47"               "gray48"             
[202] "gray49"               "gray50"               "gray51"             
[205] "gray52"               "gray53"               "gray54"             
[208] "gray55"               "gray56"               "gray57"             
[211] "gray58"               "gray59"               "gray60"             
[214] "gray61"               "gray62"               "gray63"             
[217] "gray64"               "gray65"               "gray66"             
[220] "gray67"               "gray68"               "gray69"             
[223] "gray70"               "gray71"               "gray72"             
[226] "gray73"               "gray74"               "gray75"             
[229] "gray76"               "gray77"               "gray78"             
[232] "gray79"               "gray80"               "gray81"             
[235] "gray82"               "gray83"               "gray84"             
[238] "gray85"               "gray86"               "gray87"             
[241] "gray88"               "gray89"               "gray90"             
[244] "gray91"               "gray92"               "gray93"             
[247] "gray94"               "gray95"               "gray96"             
[250] "gray97"               "gray98"               "gray99"             
[253] "gray100"              "green"                "green1"             
[256] "green2"               "green3"               "green4"             
[259] "greenyellow"          "grey"                 "grey0"              
[262] "grey1"                "grey2"                "grey3"              
[265] "grey4"                "grey5"                "grey6"              
[268] "grey7"                "grey8"                "grey9"              
[271] "grey10"               "grey11"               "grey12"             
[274] "grey13"               "grey14"               "grey15"             
[277] "grey16"               "grey17"               "grey18"             
[280] "grey19"               "grey20"               "grey21"             
[283] "grey22"               "grey23"               "grey24"             
[286] "grey25"               "grey26"               "grey27"             
[289] "grey28"               "grey29"               "grey30"             
[292] "grey31"               "grey32"               "grey33"             
[295] "grey34"               "grey35"               "grey36"             
[298] "grey37"               "grey38"               "grey39"             
[301] "grey40"               "grey41"               "grey42"             
[304] "grey43"               "grey44"               "grey45"             
[307] "grey46"               "grey47"               "grey48"             
[310] "grey49"               "grey50"               "grey51"             
[313] "grey52"               "grey53"               "grey54"             
[316] "grey55"               "grey56"               "grey57"             
[319] "grey58"               "grey59"               "grey60"             
[322] "grey61"               "grey62"               "grey63"             
[325] "grey64"               "grey65"               "grey66"             
[328] "grey67"               "grey68"               "grey69"             
[331] "grey70"               "grey71"               "grey72"             
[334] "grey73"               "grey74"               "grey75"             
[337] "grey76"               "grey77"               "grey78"             
[340] "grey79"               "grey80"               "grey81"             
[343] "grey82"               "grey83"               "grey84"             
[346] "grey85"               "grey86"               "grey87"             
[349] "grey88"               "grey89"               "grey90"             
[352] "grey91"               "grey92"               "grey93"             
[355] "grey94"               "grey95"               "grey96"             
[358] "grey97"               "grey98"               "grey99"             
[361] "grey100"              "honeydew"             "honeydew1"          
[364] "honeydew2"            "honeydew3"            "honeydew4"          
[367] "hotpink"              "hotpink1"             "hotpink2"           
[370] "hotpink3"             "hotpink4"             "indianred"          
[373] "indianred1"           "indianred2"           "indianred3"         
[376] "indianred4"           "ivory"                "ivory1"             
[379] "ivory2"               "ivory3"               "ivory4"             
[382] "khaki"                "khaki1"               "khaki2"             
[385] "khaki3"               "khaki4"               "lavender"           
[388] "lavenderblush"        "lavenderblush1"       "lavenderblush2"     
[391] "lavenderblush3"       "lavenderblush4"       "lawngreen"          
[394] "lemonchiffon"         "lemonchiffon1"        "lemonchiffon2"      
[397] "lemonchiffon3"        "lemonchiffon4"        "lightblue"          
[400] "lightblue1"           "lightblue2"           "lightblue3"         
[403] "lightblue4"           "lightcoral"           "lightcyan"          
[406] "lightcyan1"           "lightcyan2"           "lightcyan3"         
[409] "lightcyan4"           "lightgoldenrod"       "lightgoldenrod1"    
[412] "lightgoldenrod2"      "lightgoldenrod3"      "lightgoldenrod4"    
[415] "lightgoldenrodyellow" "lightgray"            "lightgreen"         
[418] "lightgrey"            "lightpink"            "lightpink1"         
[421] "lightpink2"           "lightpink3"           "lightpink4"         
[424] "lightsalmon"          "lightsalmon1"         "lightsalmon2"       
[427] "lightsalmon3"         "lightsalmon4"         "lightseagreen"      
[430] "lightskyblue"         "lightskyblue1"        "lightskyblue2"      
[433] "lightskyblue3"        "lightskyblue4"        "lightslateblue"     
[436] "lightslategray"       "lightslategrey"       "lightsteelblue"     
[439] "lightsteelblue1"      "lightsteelblue2"      "lightsteelblue3"    
[442] "lightsteelblue4"      "lightyellow"          "lightyellow1"       
[445] "lightyellow2"         "lightyellow3"         "lightyellow4"       
[448] "limegreen"            "linen"                "magenta"            
[451] "magenta1"             "magenta2"             "magenta3"           
[454] "magenta4"             "maroon"               "maroon1"            
[457] "maroon2"              "maroon3"              "maroon4"            
[460] "mediumaquamarine"     "mediumblue"           "mediumorchid"       
[463] "mediumorchid1"        "mediumorchid2"        "mediumorchid3"      
[466] "mediumorchid4"        "mediumpurple"         "mediumpurple1"      
[469] "mediumpurple2"        "mediumpurple3"        "mediumpurple4"      
[472] "mediumseagreen"       "mediumslateblue"      "mediumspringgreen"  
[475] "mediumturquoise"      "mediumvioletred"      "midnightblue"       
[478] "mintcream"            "mistyrose"            "mistyrose1"         
[481] "mistyrose2"           "mistyrose3"           "mistyrose4"         
[484] "moccasin"             "navajowhite"          "navajowhite1"       
[487] "navajowhite2"         "navajowhite3"         "navajowhite4"       
[490] "navy"                 "navyblue"             "oldlace"            
[493] "olivedrab"            "olivedrab1"           "olivedrab2"         
[496] "olivedrab3"           "olivedrab4"           "orange"             
[499] "orange1"              "orange2"              "orange3"            
[502] "orange4"              "orangered"            "orangered1"         
[505] "orangered2"           "orangered3"           "orangered4"         
[508] "orchid"               "orchid1"              "orchid2"            
[511] "orchid3"              "orchid4"              "palegoldenrod"      
[514] "palegreen"            "palegreen1"           "palegreen2"         
[517] "palegreen3"           "palegreen4"           "paleturquoise"      
[520] "paleturquoise1"       "paleturquoise2"       "paleturquoise3"     
[523] "paleturquoise4"       "palevioletred"        "palevioletred1"     
[526] "palevioletred2"       "palevioletred3"       "palevioletred4"     
[529] "papayawhip"           "peachpuff"            "peachpuff1"         
[532] "peachpuff2"           "peachpuff3"           "peachpuff4"         
[535] "peru"                 "pink"                 "pink1"              
[538] "pink2"                "pink3"                "pink4"              
[541] "plum"                 "plum1"                "plum2"              
[544] "plum3"                "plum4"                "powderblue"         
[547] "purple"               "purple1"              "purple2"            
[550] "purple3"              "purple4"              "red"                
[553] "red1"                 "red2"                 "red3"               
[556] "red4"                 "rosybrown"            "rosybrown1"         
[559] "rosybrown2"           "rosybrown3"           "rosybrown4"         
[562] "royalblue"            "royalblue1"           "royalblue2"         
[565] "royalblue3"           "royalblue4"           "saddlebrown"        
[568] "salmon"               "salmon1"              "salmon2"            
[571] "salmon3"              "salmon4"              "sandybrown"         
[574] "seagreen"             "seagreen1"            "seagreen2"          
[577] "seagreen3"            "seagreen4"            "seashell"           
[580] "seashell1"            "seashell2"            "seashell3"          
[583] "seashell4"            "sienna"               "sienna1"            
[586] "sienna2"              "sienna3"              "sienna4"            
[589] "skyblue"              "skyblue1"             "skyblue2"           
[592] "skyblue3"             "skyblue4"             "slateblue"          
[595] "slateblue1"           "slateblue2"           "slateblue3"         
[598] "slateblue4"           "slategray"            "slategray1"         
[601] "slategray2"           "slategray3"           "slategray4"         
[604] "slategrey"            "snow"                 "snow1"              
[607] "snow2"                "snow3"                "snow4"              
[610] "springgreen"          "springgreen1"         "springgreen2"       
[613] "springgreen3"         "springgreen4"         "steelblue"          
[616] "steelblue1"           "steelblue2"           "steelblue3"         
[619] "steelblue4"           "tan"                  "tan1"               
[622] "tan2"                 "tan3"                 "tan4"               
[625] "thistle"              "thistle1"             "thistle2"           
[628] "thistle3"             "thistle4"             "tomato"             
[631] "tomato1"              "tomato2"              "tomato3"            
[634] "tomato4"              "turquoise"            "turquoise1"         
[637] "turquoise2"           "turquoise3"           "turquoise4"         
[640] "violet"               "violetred"            "violetred1"         
[643] "violetred2"           "violetred3"           "violetred4"         
[646] "wheat"                "wheat1"               "wheat2"             
[649] "wheat3"               "wheat4"               "whitesmoke"         
[652] "yellow"               "yellow1"              "yellow2"            
[655] "yellow3"              "yellow4"              "yellowgreen"  


plot图

tag_com<-read.table("d:/Munro1-vs-Munro2.compare.txt",header=TRUE)
plot(log10(tag_com$Munro1_RPKM[tag_com$log2_Munro2_RPKM_Munro1_RPKM>=1]),log10(tag_com$Munro2_RPKM[tag_com$log2_Munro2_RPKM_Munro1_RPKM>=1]),xlab="log10(Munro1 RPKM)",ylab="log10(Munro2 RPKM)",ylim=c(-3,3),xlim=c(-3,3),col="red",pch=".",cex=2)
points(log10(tag_com$Munro1_RPKM[tag_com$log2_Munro2_RPKM_Munro1_RPKM<=-1]),log10(tag_com$Munro2_RPKM[tag_com$log2_Munro2_RPKM_Munro1_RPKM<=-1]),col="green",pch=".",cex=2);
points(log10(tag_com$Munro1_RPKM[(tag_com$log2_Munro2_RPKM_Munro1_RPKM<1)&(tag_com$log2_Munro2_RPKM_Munro1_RPKM>-1)]),log10(tag_com$Munro2_RPKM[(tag_com$log2_Munro2_RPKM_Munro1_RPKM<1)&(tag_com$log2_Munro2_RPKM_Munro1_RPKM>-1)]),col="blue",pch=".",cex=2);
legend("topleft",legend = c("FDR <= 0.001 AND |log2Ratio| >= 1","up.regulated","down.regulated","Not DEGs"), pch = c(NULL,15,15,15),col = c("white","red","blue","green"),cex=1.1)

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