Class table example

A class defines a group of genes of interest and will be used for detailed analysis of the data.
GeneID in the first column defines the set of the GeneIDs of the "Gene Counts" (RPKM) table.
Color is used to color genes in MA and Volcano plots
Group will divide the Class in SubClasses which is used for Clustering and Correlation matrices

Example of the tab delimited Class.txt file:

GeneID ColorGroup
llmg_0022greenCarbohydrate metabolism
llmg_0023greenCarbohydrate metabolism
llmg_0024greenCarbohydrate metabolism
llmg_0025greenCarbohydrate metabolism
llmg_0442redDNA replication
llmg_0443redDNA replication
llmg_0444redDNA replication
llmg_0445redDNA replication
llmg_0446redDNA replication
llmg_0447redDNA replication
llmg_0448redDNA replication
llmg_0449redDNA replication
llmg_0450redDNA replication
llmg_0451redDNA replication
llmg_0452redHelix-turn-helix GntR family
llmg_0453redHelix-turn-helix GntR family
llmg_0454redHelix-turn-helix GntR family
llmg_0455redHelix-turn-helix GntR family


Link to the example file (right click the mouse to download this file)

A full list of colors that can be used:
white darkred gray46 grey37 lemonchiffon3 olivedrab3 slateblue1
aliceblue darksalmon gray47 grey38 lemonchiffon4 olivedrab4 slateblue2
antiquewhite darkseagreen gray48 grey39 lightblue orange slateblue3
antiquewhite1 darkseagreen1 gray49 grey40 lightblue1 orange1 slateblue4
antiquewhite2 darkseagreen2 gray50 grey41 lightblue2 orange2 slategray
antiquewhite3 darkseagreen3 gray51 grey42 lightblue3 orange3 slategray1
antiquewhite4 darkseagreen4 gray52 grey43 lightblue4 orange4 slategray2
aquamarine darkslateblue gray53 grey44 lightcoral orangered slategray3
aquamarine1 darkslategray gray54 grey45 lightcyan orangered1 slategray4
aquamarine2 darkslategray1 gray55 grey46 lightcyan1 orangered2 slategrey
aquamarine3 darkslategray2 gray56 grey47 lightcyan2 orangered3 snow
aquamarine4 darkslategray3 gray57 grey48 lightcyan3 orangered4 snow1
azure darkslategray4 gray58 grey49 lightcyan4 orchid snow2
azure1 darkslategrey gray59 grey50 lightgoldenrod orchid1 snow3
azure2 darkturquoise gray60 grey51 lightgoldenrod1 orchid2 snow4
azure3 darkviolet gray61 grey52 lightgoldenrod2 orchid3 springgreen
azure4 deeppink gray62 grey53 lightgoldenrod3 orchid4 springgreen1
beige deeppink1 gray63 grey54 lightgoldenrod4 palegoldenrod springgreen2
bisque deeppink2 gray64 grey55 lightgoldenrodyellow palegreen springgreen3
bisque1 deeppink3 gray65 grey56 lightgray palegreen1 springgreen4
bisque2 deeppink4 gray66 grey57 lightgreen palegreen2 steelblue
bisque3 deepskyblue gray67 grey58 lightgrey palegreen3 steelblue1
bisque4 deepskyblue1 gray68 grey59 lightpink palegreen4 steelblue2
black deepskyblue2 gray69 grey60 lightpink1 paleturquoise steelblue3
blanchedalmond deepskyblue3 gray70 grey61 lightpink2 paleturquoise1 steelblue4
blue deepskyblue4 gray71 grey62 lightpink3 paleturquoise2 tan
blue1 dimgray gray72 grey63 lightpink4 paleturquoise3 tan1
blue2 dimgrey gray73 grey64 lightsalmon paleturquoise4 tan2
blue3 dodgerblue gray74 grey65 lightsalmon1 palevioletred tan3
blue4 dodgerblue1 gray75 grey66 lightsalmon2 palevioletred1 tan4
blueviolet dodgerblue2 gray76 grey67 lightsalmon3 palevioletred2 thistle
brown dodgerblue3 gray77 grey68 lightsalmon4 palevioletred3 thistle1
brown1 dodgerblue4 gray78 grey69 lightseagreen palevioletred4 thistle2
brown2 firebrick gray79 grey70 lightskyblue papayawhip thistle3
brown3 firebrick1 gray80 grey71 lightskyblue1 peachpuff thistle4
brown4 firebrick2 gray81 grey72 lightskyblue2 peachpuff1 tomato
burlywood firebrick3 gray82 grey73 lightskyblue3 peachpuff2 tomato1
burlywood1 firebrick4 gray83 grey74 lightskyblue4 peachpuff3 tomato2
burlywood2 floralwhite gray84 grey75 lightslateblue peachpuff4 tomato3
burlywood3 forestgreen gray85 grey76 lightslategray peru tomato4
burlywood4 gainsboro gray86 grey77 lightslategrey pink turquoise
cadetblue ghostwhite gray87 grey78 lightsteelblue pink1 turquoise1
cadetblue1 gold gray88 grey79 lightsteelblue1 pink2 turquoise2
cadetblue2 gold1 gray89 grey80 lightsteelblue2 pink3 turquoise3
cadetblue3 gold2 gray90 grey81 lightsteelblue3 pink4 turquoise4
cadetblue4 gold3 gray91 grey82 lightsteelblue4 plum violet
chartreuse gold4 gray92 grey83 lightyellow plum1 violetred
chartreuse1 goldenrod gray93 grey84 lightyellow1 plum2 violetred1
chartreuse2 goldenrod1 gray94 grey85 lightyellow2 plum3 violetred2
chartreuse3 goldenrod2 gray95 grey86 lightyellow3 plum4 violetred3
chartreuse4 goldenrod3 gray96 grey87 lightyellow4 powderblue violetred4
chocolate goldenrod4 gray97 grey88 limegreen purple wheat
chocolate1 gray gray98 grey89 linen purple1 wheat1
chocolate2 gray0 gray99 grey90 magenta purple2 wheat2
chocolate3 gray1 gray100 grey91 magenta1 purple3 wheat3
chocolate4 gray2 green grey92 magenta2 purple4 wheat4
coral gray3 green1 grey93 magenta3 red whitesmoke
coral1 gray4 green2 grey94 magenta4 red1 yellow
coral2 gray5 green3 grey95 maroon red2 yellow1
coral3 gray6 green4 grey96 maroon1 red3 yellow2
coral4 gray7 greenyellow grey97 maroon2 red4 yellow3
cornflowerblue gray8 grey grey98 maroon3 rosybrown yellow4
cornsilk gray9 grey0 grey99 maroon4 rosybrown1 yellowgreen
cornsilk1 gray10 grey1 grey100 mediumaquamarine rosybrown2
cornsilk2 gray11 grey2 honeydew mediumblue rosybrown3
cornsilk3 gray12 grey3 honeydew1 mediumorchid rosybrown4
cornsilk4 gray13 grey4 honeydew2 mediumorchid1 royalblue
cyan gray14 grey5 honeydew3 mediumorchid2 royalblue1
cyan1 gray15 grey6 honeydew4 mediumorchid3 royalblue2
cyan2 gray16 grey7 hotpink mediumorchid4 royalblue3
cyan3 gray17 grey8 hotpink1 mediumpurple royalblue4
cyan4 gray18 grey9 hotpink2 mediumpurple1 saddlebrown
darkblue gray19 grey10 hotpink3 mediumpurple2 salmon
darkcyan gray20 grey11 hotpink4 mediumpurple3 salmon1
darkgoldenrod gray21 grey12 indianred mediumpurple4 salmon2
darkgoldenrod1 gray22 grey13 indianred1 mediumseagreen salmon3
darkgoldenrod2 gray23 grey14 indianred2 mediumslateblue salmon4
darkgoldenrod3 gray24 grey15 indianred3 mediumspringgreen sandybrown
darkgoldenrod4 gray25 grey16 indianred4 mediumturquoise seagreen
darkgray gray26 grey17 ivory mediumvioletred seagreen1
darkgreen gray27 grey18 ivory1 midnightblue seagreen2
darkgrey gray28 grey19 ivory2 mintcream seagreen3
darkkhaki gray29 grey20 ivory3 mistyrose seagreen4
darkmagenta gray30 grey21 ivory4 mistyrose1 seashell
darkolivegreen gray31 grey22 khaki mistyrose2 seashell1
darkolivegreen1 gray32 grey23 khaki1 mistyrose3 seashell2
darkolivegreen2 gray33 grey24 khaki2 mistyrose4 seashell3
darkolivegreen3 gray34 grey25 khaki3 moccasin seashell4
darkolivegreen4 gray35 grey26 khaki4 navajowhite sienna
darkorange gray36 grey27 lavender navajowhite1 sienna1
darkorange1 gray37 grey28 lavenderblush navajowhite2 sienna2
darkorange2 gray38 grey29 lavenderblush1 navajowhite3 sienna3
darkorange3 gray39 grey30 lavenderblush2 navajowhite4 sienna4
darkorange4 gray40 grey31 lavenderblush3 navy skyblue
darkorchid gray41 grey32 lavenderblush4 navyblue skyblue1
darkorchid1 gray42 grey33 lawngreen oldlace skyblue2
darkorchid2 gray43 grey34 lemonchiffon olivedrab skyblue3
darkorchid3 gray44 grey35 lemonchiffon1 olivedrab1 skyblue4
darkorchid4 gray45 grey36 lemonchiffon2 olivedrab2 slateblue