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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 |字号大中小订阅

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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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    </ul>
    {/if}

<#--引用记录--> <#--博主推荐--> <#--随机阅读--> <#--首页推荐--> <#--历史上的今天--> <#--被推荐日志--> <#--上一篇，下一篇--> <#-- 热度 -->

{list a as x}
    {if !!x}
    <div class="hotItem iblock nbw-fce nbw-f40">
      <a class="fc03 noul" target="_blank" hidefocus="true" href="http://blog.163.com/${x.publisherUsername}/">
      {if x.publisherUsername==visitor.userName}
      <img alt="${x.publisherNickname|escape}" onerror="this.src=location.f40" class="cwd bdwa bdc0" src="${fn1(x.publisherUsername)}&r=${visitor.imageUpdateTime}"/>
      {else}
      <img alt="${x.publisherNickname|escape}" onerror="this.src=location.f40" class="cwd bdwa bdc0" src="${fn1(x.publisherUsername)}"/>
      {/if}
      </a>
      <div class="cwd vname thide">
        <a class="fc03 m2a"  target="_blank" hidefocus="true" href="http://blog.163.com/${x.publisherUsername}/">
          ${fn(x.publisherNickname,8)|escape}
        </a>
      </div>
      <a class="f-myLikeIcons hottype {if x.type==1} js-liketype{elseif x.type==2} js-reblogtype{elseif x.type==3} js-sharetype{else}{/if}" target="_blank" hidefocus="true" href="http://blog.163.com/${x.publisherUsername}/"> </a>
    </div>
    {/if}
    {/list}

<#-- 网易新闻广告 --> <#--右边模块结构--> <#--评论模块结构--> <#--引用模块结构--> <#--博主发起的投票-->

页脚

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云之南

导航

日志

R 的颜色设置与包及MAplot及scatterplots图

历史上的今天

最近读者

热度

评论

页脚