Dear all, i try to plot with ggplot2. Therefor I have an matrix with 3 colums. With cbind I add an additional column called "col". I need this column "col" because in a later step and want to specify here some plot details which I will get from another analysis If I want to plot with this code, I have the problem that the legend is wrong. Blue changed to green and green to blue. Furthermore the colors in the plot seem a little bit strange. Can anybody help me out? All the best and thanks Peter #####THE CODE p0 <- ggplot(DATA, aes(Freq, Var1)) p1 <- p0+ geom_point(aes(Freq, reorder(Var1, rep(score,cl.count)), colour=col)) p2 <- p1 +geom_segment(aes(x = 0, xend = Freq, y = Var1, yend = Var1, colour=col)) p3 <- p2 + facet_grid(.~Var2) plot(p3) #### THE DATA # #class(DATA) = data.frame #class(DATA$Var1) = class(DATA$Var2) = factor #class(DATA$Freq) = numeric #class(DATA$col) = character Var1 Var2 Freq col 1 208869_s_at JT 10.6802376685463 blue 2 203394_s_at JT 10.0160470327077 blue 3 201533_at JT 9.58401500697783 blue 4 216520_s_at JT 9.07764840614892 blue 5 210999_s_at JT 9.00219110130877 green 6 212284_x_at JT 8.62193952504277 blue 7 203752_s_at JT 8.69193736253539 green 8 203574_at JT 8.41492571590263 blue 9 219629_at JT 8.19111292436667 blue 10 201473_at JT 8.035082989931 green 11 210592_s_at JT 8.00639829720742 green 12 200768_s_at JT 7.88012483915651 green 13 201565_s_at JT 7.89885432096935 green 14 AFFX-r2-P1-cre-3_at JT 7.86490927895639 blue 15 202014_at JT 7.69345791769434 green 16 212671_s_at JT -7.43350555284605 green 17 203395_s_at JT 7.51127977823914 blue 18 208980_s_at JT 7.52175408445448 blue 19 207783_x_at JT 7.31954223019292 blue 20 215446_s_at JT -6.28236730203077 green 21 203034_s_at JT 7.24582647671987 blue 22 211943_x_at JT 7.22247828112639 green 23 203974_at JT -6.84217612309489 green 24 201810_s_at JT 7.0727443704914 green 25 201693_s_at JT 7.11350154823655 blue 26 213614_x_at JT 7.07586402329325 green 27 AFFX-CreX-5_at JT 7.05274590106307 blue 28 201798_s_at JT -6.98858491240942 blue 29 212869_x_at JT 6.97833756793094 green 30 201531_at JT 6.96660504363297 green 31 201170_s_at JT 6.90904695259236 green 32 200886_s_at JT -6.92645789612039 blue 33 AFFX-r2-P1-cre-5_at JT 6.85399276205727 blue 34 201429_s_at JT 6.68557384216737 green 35 212665_at JT 6.75579868986925 green 36 208695_s_at JT 6.8087149011011 green 37 211654_x_at JT -6.7426888322764 green 38 209927_s_at JT -6.74856557366229 green 39 203107_x_at JT 6.72120597236789 blue 40 211296_x_at JT 6.60226581063165 green 41 208869_s_at OA -3.73983541027906 green 42 203394_s_at OA -3.29203821581412 green 43 201533_at OA -3.2383756900468 blue 44 216520_s_at OA -4.59979375515969 blue 45 210999_s_at OA -5.10853597491871 green 46 212284_x_at OA -5.84925048581651 blue 47 203752_s_at OA -4.54427623838229 blue 48 203574_at OA -2.59882534850623 blue 49 219629_at OA -4.35550869055387 blue 50 201473_at OA -3.15685663855675 blue 51 210592_s_at OA -4.52611461089035 blue 52 200768_s_at OA -2.76833454650619 blue 53 201565_s_at OA -3.80972141262264 green 54 AFFX-r2-P1-cre-3_at OA -3.53240421347696 green 55 202014_at OA -2.60784960582222 blue 56 212671_s_at OA 1.68584117381632 green 57 203395_s_at OA -2.27910272551108 blue 58 208980_s_at OA -3.66266591800146 green 59 207783_x_at OA -3.93093352561262 blue 60 215446_s_at OA 6.26626194024723 green 61 203034_s_at OA -3.84606488854982 blue 62 211943_x_at OA -3.30831181470312 green 63 203974_at OA 1.17068337099947 green 64 201810_s_at OA -2.07855331860079 green 65 201693_s_at OA -2.74740330465003 blue 66 213614_x_at OA -3.03851670866666 blue 67 AFFX-CreX-5_at OA -3.46221400689819 green 68 201798_s_at OA 4.03100733638473 green 69 212869_x_at OA -3.97300711584927 green 70 201531_at OA -2.96907452702537 green 71 201170_s_at OA -2.70131412682545 green 72 200886_s_at OA 2.96401783822817 blue 73 AFFX-r2-P1-cre-5_at OA -2.89903293592039 blue 74 201429_s_at OA -4.35557947874114 blue 75 212665_at OA -2.39194028704917 blue 76 208695_s_at OA -3.35547642329559 green 77 211654_x_at OA 2.68663713811722 green 78 209927_s_at OA 3.34341605878591 blue 79 203107_x_at OA -3.66321419312914 blue 80 211296_x_at OA -4.25932160076237 green 81 208869_s_at RA -6.52772554526193 green 82 203394_s_at RA -6.32419887021955 green 83 201533_at RA -5.96832724224416 blue 84 216520_s_at RA -4.21160115876773 blue 85 210999_s_at RA -3.662138171127 green 86 212284_x_at RA -2.60782479125985 blue 87 203752_s_at RA -3.90104095781671 green 88 203574_at RA -5.47027470876589 blue 89 219629_at RA -3.60753898792399 green 90 201473_at RA -4.58816673507709 green 91 210592_s_at RA -3.27334582039087 blue 92 200768_s_at RA -4.80784295112116 blue 93 201565_s_at RA -3.8459928330509 blue 94 AFFX-r2-P1-cre-3_at RA -4.07489406787897 green 95 202014_at RA -4.7832177524091 green 96 212671_s_at RA 5.40590792815972 green 97 203395_s_at RA -4.92107150759781 blue 98 208980_s_at RA -3.62962656459378 green 99 207783_x_at RA -3.18712183828209 blue 100 215446_s_at RA 0.0151477360559071 blue 101 203034_s_at RA -3.19761157077928 blue 102 211943_x_at RA -3.68142990571529 blue 103 203974_at RA 5.33426547049511 green 104 201810_s_at RA -4.69723616790538 blue 105 201693_s_at RA -4.10648979370521 green 106 213614_x_at RA -3.79728641367864 blue 107 AFFX-CreX-5_at RA -3.37703866352978 green 108 201798_s_at RA 2.78171984514488 green 109 212869_x_at RA -2.8266333324756 blue 110 201531_at RA -3.7598371247344 green 111 201170_s_at RA -3.95754079263605 green 112 200886_s_at RA 3.72683314668998 blue 113 AFFX-r2-P1-cre-5_at RA -3.71979768994025 blue 114 201429_s_at RA -2.19145276606072 green 115 212665_at RA -4.10438313399814 blue 116 208695_s_at RA -3.24790872151558 green 117 211654_x_at RA 3.81487862974044 blue 118 209927_s_at RA 3.20267913105723 green 119 203107_x_at RA -2.87616341412488 blue 120 211296_x_at RA -2.20363261389773 green [[alternative HTML version deleted]]

Hi Peter, below a small example that I think creates what you want: ggplot( data.frame( value=rnorm(100), rank=1:100, col=rep(c("blue","green"), 50) ) ) + geom_point( aes(y=value, x=rank, colour=col, shape=col) ) + scale_colour_manual( values=c("blue","green") ) The result looks like this for me: http://www-huber.embl.de/users/pyl/example/ggplot_example.png Cheers, Paul On 11/22/2012 03:33 PM, Peter Kupfer wrote: > Dear all, > i try to plot with ggplot2. Therefor I have an matrix with 3 colums. With cbind I add an additional column called "col". I need this column "col" because in a later step and want to specify here some plot details which I will get from another analysis > If I want to plot with this code, I have the problem that the legend is wrong. > Blue changed to green and green to blue. Furthermore the colors in the plot seem a little bit strange. Can anybody help me out? > All the best and thanks > Peter > > > > #####THE CODE > > > p0 <- ggplot(DATA, aes(Freq, Var1)) > p1 <- p0+ geom_point(aes(Freq, reorder(Var1, rep(score,cl.count)), colour=col)) > > p2 <- p1 +geom_segment(aes(x = 0, xend = Freq, y = Var1, yend = Var1, colour=col)) > p3 <- p2 + facet_grid(.~Var2) > plot(p3) > > > > #### THE DATA # > > #class(DATA) = data.frame > #class(DATA$Var1) = class(DATA$Var2) = factor > > #class(DATA$Freq) = numeric > #class(DATA$col) = character > > Var1 Var2 Freq col > 1 208869_s_at JT 10.6802376685463 blue > 2 203394_s_at JT 10.0160470327077 blue > 3 201533_at JT 9.58401500697783 blue > 4 216520_s_at JT 9.07764840614892 blue > 5 210999_s_at JT 9.00219110130877 green > 6 212284_x_at JT 8.62193952504277 blue > 7 203752_s_at JT 8.69193736253539 green > 8 203574_at JT 8.41492571590263 blue > 9 219629_at JT 8.19111292436667 blue > 10 201473_at JT 8.035082989931 green > 11 210592_s_at JT 8.00639829720742 green > 12 200768_s_at JT 7.88012483915651 green > 13 201565_s_at JT 7.89885432096935 green > 14 AFFX-r2-P1-cre-3_at JT 7.86490927895639 blue > 15 202014_at JT 7.69345791769434 green > 16 212671_s_at JT -7.43350555284605 green > 17 203395_s_at JT 7.51127977823914 blue > 18 208980_s_at JT 7.52175408445448 blue > 19 207783_x_at JT 7.31954223019292 blue > 20 215446_s_at JT -6.28236730203077 green > 21 203034_s_at JT 7.24582647671987 blue > 22 211943_x_at JT 7.22247828112639 green > 23 203974_at JT -6.84217612309489 green > 24 201810_s_at JT 7.0727443704914 green > 25 201693_s_at JT 7.11350154823655 blue > 26 213614_x_at JT 7.07586402329325 green > 27 AFFX-CreX-5_at JT 7.05274590106307 blue > 28 201798_s_at JT -6.98858491240942 blue > 29 212869_x_at JT 6.97833756793094 green > 30 201531_at JT 6.96660504363297 green > 31 201170_s_at JT 6.90904695259236 green > 32 200886_s_at JT -6.92645789612039 blue > 33 AFFX-r2-P1-cre-5_at JT 6.85399276205727 blue > 34 201429_s_at JT 6.68557384216737 green > 35 212665_at JT 6.75579868986925 green > 36 208695_s_at JT 6.8087149011011 green > 37 211654_x_at JT -6.7426888322764 green > 38 209927_s_at JT -6.74856557366229 green > 39 203107_x_at JT 6.72120597236789 blue > 40 211296_x_at JT 6.60226581063165 green > 41 208869_s_at OA -3.73983541027906 green > 42 203394_s_at OA -3.29203821581412 green > 43 201533_at OA -3.2383756900468 blue > 44 216520_s_at OA -4.59979375515969 blue > 45 210999_s_at OA -5.10853597491871 green > 46 212284_x_at OA -5.84925048581651 blue > 47 203752_s_at OA -4.54427623838229 blue > 48 203574_at OA -2.59882534850623 blue > 49 219629_at OA -4.35550869055387 blue > 50 201473_at OA -3.15685663855675 blue > 51 210592_s_at OA -4.52611461089035 blue > 52 200768_s_at OA -2.76833454650619 blue > 53 201565_s_at OA -3.80972141262264 green > 54 AFFX-r2-P1-cre-3_at OA -3.53240421347696 green > 55 202014_at OA -2.60784960582222 blue > 56 212671_s_at OA 1.68584117381632 green > 57 203395_s_at OA -2.27910272551108 blue > 58 208980_s_at OA -3.66266591800146 green > 59 207783_x_at OA -3.93093352561262 blue > 60 215446_s_at OA 6.26626194024723 green > 61 203034_s_at OA -3.84606488854982 blue > 62 211943_x_at OA -3.30831181470312 green > 63 203974_at OA 1.17068337099947 green > 64 201810_s_at OA -2.07855331860079 green > 65 201693_s_at OA -2.74740330465003 blue > 66 213614_x_at OA -3.03851670866666 blue > 67 AFFX-CreX-5_at OA -3.46221400689819 green > 68 201798_s_at OA 4.03100733638473 green > 69 212869_x_at OA -3.97300711584927 green > 70 201531_at OA -2.96907452702537 green > 71 201170_s_at OA -2.70131412682545 green > 72 200886_s_at OA 2.96401783822817 blue > 73 AFFX-r2-P1-cre-5_at OA -2.89903293592039 blue > 74 201429_s_at OA -4.35557947874114 blue > 75 212665_at OA -2.39194028704917 blue > 76 208695_s_at OA -3.35547642329559 green > 77 211654_x_at OA 2.68663713811722 green > 78 209927_s_at OA 3.34341605878591 blue > 79 203107_x_at OA -3.66321419312914 blue > 80 211296_x_at OA -4.25932160076237 green > 81 208869_s_at RA -6.52772554526193 green > 82 203394_s_at RA -6.32419887021955 green > 83 201533_at RA -5.96832724224416 blue > 84 216520_s_at RA -4.21160115876773 blue > 85 210999_s_at RA -3.662138171127 green > 86 212284_x_at RA -2.60782479125985 blue > 87 203752_s_at RA -3.90104095781671 green > 88 203574_at RA -5.47027470876589 blue > 89 219629_at RA -3.60753898792399 green > 90 201473_at RA -4.58816673507709 green > 91 210592_s_at RA -3.27334582039087 blue > 92 200768_s_at RA -4.80784295112116 blue > 93 201565_s_at RA -3.8459928330509 blue > 94 AFFX-r2-P1-cre-3_at RA -4.07489406787897 green > 95 202014_at RA -4.7832177524091 green > 96 212671_s_at RA 5.40590792815972 green > 97 203395_s_at RA -4.92107150759781 blue > 98 208980_s_at RA -3.62962656459378 green > 99 207783_x_at RA -3.18712183828209 blue > 100 215446_s_at RA 0.0151477360559071 blue > 101 203034_s_at RA -3.19761157077928 blue > 102 211943_x_at RA -3.68142990571529 blue > 103 203974_at RA 5.33426547049511 green > 104 201810_s_at RA -4.69723616790538 blue > 105 201693_s_at RA -4.10648979370521 green > 106 213614_x_at RA -3.79728641367864 blue > 107 AFFX-CreX-5_at RA -3.37703866352978 green > 108 201798_s_at RA 2.78171984514488 green > 109 212869_x_at RA -2.8266333324756 blue > 110 201531_at RA -3.7598371247344 green > 111 201170_s_at RA -3.95754079263605 green > 112 200886_s_at RA 3.72683314668998 blue > 113 AFFX-r2-P1-cre-5_at RA -3.71979768994025 blue > 114 201429_s_at RA -2.19145276606072 green > 115 212665_at RA -4.10438313399814 blue > 116 208695_s_at RA -3.24790872151558 green > 117 211654_x_at RA 3.81487862974044 blue > 118 209927_s_at RA 3.20267913105723 green > 119 203107_x_at RA -2.87616341412488 blue > 120 211296_x_at RA -2.20363261389773 green > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor@r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor [[alternative HTML version deleted]]