[R] boxplots facets in ggplot, generated with two factors interaction mediane-ordered

Bert Gunter bgunter.4567 at gmail.com
Mon Sep 7 00:09:14 CEST 2015


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Bert Gunter


Bert Gunter

"Data is not information. Information is not knowledge. And knowledge
is certainly not wisdom."
   -- Clifford Stoll


On Sun, Sep 6, 2015 at 8:37 AM, Sergio Fonda <sergio.fonda99 at gmail.com> wrote:
> Thanks to Marc Schwartz I was able to order a "two factors"
> interaction boxplot with median associated to one factor alone.
> I tried further to generate facets plot (3x2 boxplots in ggplot2) for the
> dataframe reported at bottom and I'm not able to reach a correct plot.
> The dataframe is a simulation of genes expressions in five conditions of
> patients.
> I would like that each of the 5 boxplots were ordered with median of values
> associated to the combination "gene*pat.cond".
> Any help is much appreciated,
> Sergio
>  ____________________________
> Example Dataframe:
>     pat.cond     gene        value
> 1          N  ADAMTS1 -5.557194292
> 2          N  ADAMTS1 -2.576700157
> 3          E  ADAMTS1 -6.629356620
> 4          E  ADAMTS1 -6.629356620
> 5          E  ADAMTS1 -6.629356620
> 6          E  ADAMTS1 -6.629356620
> 7          M  ADAMTS1 -6.629356620
> 8          M  ADAMTS1 -6.629356620
> 9          M  ADAMTS1 -6.629356620
> 10         M  ADAMTS1 -2.742163709
> 11         N ADAMTS12 -1.084104611
> 12         E ADAMTS12  1.710871953
> 13         E ADAMTS12  6.629356620
> 14         M ADAMTS12  6.629356620
> 15         M ADAMTS12  1.711422682
> 16         E      APC -3.665169008
> 17         E      APC -1.192183578
> 18         M      APC -6.629356620
> 19         M      APC  3.696542194
> 20         M      APC -3.533991641
> 21         R      APC -4.267887134
> 22         N    BORIS  6.629356620
> 23         E    BORIS  6.629356620
> 24         M    BORIS  6.629356620
> 25         M    BORIS  6.629356620
> 26         M    BORIS  6.629356620
> 27         S    BORIS  6.629356620
> 28         E    BRCA1 -4.260347862
> 29         E    BRCA1 -6.629356620
> 30         E    BRCA1 -6.629356620
> 31         M    BRCA1 -6.443174967
> 32         M    BRCA1 -6.629356620
> 33         M    BRCA1 -6.629356620
> 34         M    BRCA1 -2.525972281
> 35         N      P16 -1.698706675
> 36         M      P16 -6.629356620
> 37         M      P16 -6.629356620
> 38         M      P16 -6.629356620
> 39         S      P16 -6.629356620
> 40         S      P16 -6.629356620
> 41         S      P16  0.518269571
> 42         N     DAX1  0.708010228
> 43         E     DAX1 -0.337455350
> 44         E     DAX1  2.803374605
> 45         E     DAX1 -1.407226228
> 46         M     DAX1  6.629356620
> 47         S     DAX1  2.022408499
> 48         S     DAX1  6.629356620
> 49         S     DAX1  6.629356620
> 50         S     DAX1  6.629356620
> 51         N     DKK1 -0.876905559
> 52         N     DKK1  0.008176565
> 53         E     DKK1 -3.057081024
> 54         M     DKK1  0.804046915
> 55         N     DKK2 -4.677880676
> 56         N     DKK2 -3.264182143
> 57         M     DKK2  0.219772061
> 58         R     DKK2 -3.205760419
> 59         R     DKK2 -3.567799537
> 60         R     DKK2 -1.687113091
> 61         S     DKK2 -6.629356620
> 62         S     DKK2 -6.629356620
> 63         N     ESR1  1.479810020
> 64         M     ESR1  1.861011014
> 65         N     FBP1 -0.110196473
> 66         N     FBP1  0.721286184
> 67         E     FBP1 -5.107943868
> 68         E     FBP1 -4.593812366
> 69         M     FBP1 -1.622176688
> 70         S     FBP1 -3.097791525
> 71         E    FOXL2 -4.564123239
> 72         E    FOXL2  3.111180437
> 73         M    FOXL2  0.323703764
> 74         M    FOXL2 -3.851350485
> 75         R    FOXL2 -3.324087523
> 76         S    FOXL2  0.739408989
> 77         M    GATA5 -1.171932246
> 78         M    GATA5 -3.466054731
> 79         M    GATA5 -1.283038699
> 80         S    GATA5 -2.778390690
> 81         S    GATA5 -2.014479273
> 82         S    GATA5 -3.015234172
> 83         E     GPX3 -6.629356620
> 84         E     GPX3 -1.942190735
> 85         M     GPX3  6.629356620
> 86         M     GPX3 -6.629356620
> 87         M     GPX3 -2.615982450
> 88         M     GPX3 -6.629356620
> 89         M     GPX3  0.128743354
> 90         S     GPX3 -6.629356620
> 91         E      MAL -6.629356620
> 92         E      MAL -4.825545452
> 93         E      MAL -6.629356620
> 94         E      MAL -6.629356620
> 95         E      MAL -6.629356620
> 96         M      MAL -0.419005364
> 97         M      MAL -0.923667455
> 98         M      MAL  6.629356620
> 99         M      MAL  3.371740196
> 100        S      MAL -6.629356620
> 101        N     MGMT -6.629356620
> 102        E     MGMT  1.115112556
> 103        M     MGMT  4.030893797
> 104        S     MGMT -6.629356620
> 105        N     MLH1 -0.519875304
> 106        N     MLH1 -1.352872084
> 107        E     MLH1 -0.777864442
> 108        E     MLH1  1.105073029
> 109        E     MLH1  5.758699199
> 110        E     MLH1 -1.498072236
> 111        S     MLH1 -1.630362301
> 112        M    MYOD1 -6.629356620
> 113        M    MYOD1  6.629356620
> 114        M    MYOD1 -6.629356620
> 115        M    MYOD1 -6.629356620
> 116        R    MYOD1 -6.629356620
> 117        R    MYOD1 -6.629356620
> 118        S    MYOD1 -6.629356620
> 119        S    MYOD1 -6.629356620
> 120        S    MYOD1 -4.645053781
> 121        N    NELL1 -6.629356620
> 122        N    NELL1 -5.536591557
> 123        N    NELL1 -5.903856552
> 124        E    NELL1 -6.629356620
> 125        E    NELL1 -6.629356620
> 126        M    NELL1 -6.629356620
> 127        S    NELL1 -6.629356620
> 128        N     OSMR -6.629356620
> 129        M     OSMR  4.407821839
> 130        M     OSMR  0.364604851
> 131        M     OSMR -6.629356620
> 132        S     OSMR -6.629356620
> 133        N     PAX6  6.629356620
> 134        E     PAX6 -3.401030959
> 135        M     PAX6 -0.946878855
> 136        S     PAX6  0.964721065
> 137        E    PTGS2 -3.749795240
> 138        M    PTGS2 -6.629356620
> 139        S    PTGS2 -2.076356656
> 140        S    PTGS2 -3.961164916
> 141        N     RARB -4.611429173
> 142        E     RARB -1.706166432
> 143        S     RARB -3.697493231
> 144        N  RASSF1A -1.505128642
> 145        E  RASSF1A  0.808179628
> 146        E  RASSF1A -6.629356620
> 147        E  RASSF1A -0.694997778
> 148        M  RASSF1A -0.332307577
> 149        S  RASSF1A -6.629356620
> 150        S  RASSF1A  6.629356620
> 151        N     RPRM -4.023523466
> 152        E     RPRM  0.443243995
> 153        S     RPRM -6.629356620
> 154        S     RPRM -4.019270038
> 155        E    RSPOI -1.735307607
> 156        E    RSPOI -1.296083205
> 157        M    RSPOI -3.003752756
> 158        S    RSPOI -3.156564936
> 159        S    RSPOI -2.928871731
> 160        N  SEPTIN9 -6.629356620
> 161        E  SEPTIN9 -2.585469731
> 162        E  SEPTIN9 -2.525798264
> 163        M  SEPTIN9  6.629356620
> 164        R  SEPTIN9 -3.071222253
> 165        S  SEPTIN9 -6.629356620
> 166        M    SFRP1 -1.426465815
> 167        R    SFRP1 -6.629356620
> 168        S    SFRP1 -2.348648751
> 169        S    SFRP1 -6.629356620
> 170        S    SFRP1 -2.304295273
> 171        N    SFRP4 -2.315044901
> 172        E    SFRP4 -2.940158139
> 173        M    SFRP4  6.629356620
> 174        S    SFRP4 -6.629356620
> 175        S    SFRP4  6.629356620
> 176        N    SFRP5 -6.629356620
> 177        E    SFRP5 -5.833523393
> 178        E    SFRP5  2.765666156
> 179        E    SFRP5  2.707734922
> 180        E    SFRP5  6.629356620
> 181        M    SMAD4 -6.629356620
> 182        M    SMAD4 -6.629356620
> 183        M    SMAD4 -6.629356620
> 184        R    SMAD4 -6.629356620
> 185        S    SMAD4 -6.629356620
> 186        S    SMAD4 -6.629356620
> 187        S    SMAD4 -6.629356620
> 188        N    SOCS3 -0.604614698
> 189        N    SOCS3  0.097268646
> 190        E    SOCS3 -1.505450218
> 191        E    SOCS3  6.629356620
> 192        N    SPARC -3.865639988
> 193        N    SPARC -1.868782928
> 194        E    SPARC  2.821046068
> 195        E    SPARC  6.629356620
> 196        S    SPARC -6.629356620
> 197        S    SPARC  0.202017887
> 198        S    SPARC  6.629356620
> 199        S    SPARC  6.629356620
> 200        N     TAC1 -1.528221578
> 201        M     TAC1  6.629356620
> 202        M     TAC1  6.629356620
> 203        R     TAC1 -2.294267250
> 204        S     TAC1  2.624594634
> 205        N     TERT -2.985641232
> 206        E     TERT  2.809747729
> 207        E     TERT  6.629356620
> 208        E     TERT -3.164404633
> 209        M     TERT  6.629356620
> 210        M     TERT -2.766881108
> 211        S     TERT  0.875337372
> 212        S     TERT  3.175095461
> 213        N    TIMP3 -2.046729298
> 214        E    TIMP3 -3.461408230
> 215        E    TIMP3 -2.996720557
> 216        M    TIMP3 -6.629356620
> 217        M    TIMP3 -1.527333149
> 218        R    TIMP3 -3.933657283
> 219        S    TIMP3 -1.020144976
> 220        S    TIMP3 -2.357112874
> 221        S    TIMP3  0.806736362
> 222        M   TMEFF2 -1.160275850
> 223        M   TMEFF2 -2.712025806
> 224        R   TMEFF2 -3.961478237
> 225        R   TMEFF2 -6.510953714
> 226        S   TMEFF2 -0.619555286
> 227        S   TMEFF2  2.344341057
> 228        E     WIF1 -6.629356620
> 229        E     WIF1 -3.806114522
> 230        E     WIF1 -2.318313158
> 231        M     WIF1  1.102899897
> 232        M     WIF1  6.629356620
> 233        M     WIF1 -6.629356620
> 234        N     WNT4 -6.629356620
> 235        E     WNT4 -3.474027185
> 236        E     WNT4 -6.629356620
> 237        S     WNT4 -6.629356620
> 238        S     WNT4 -6.629356620
> 239        E      WRN -6.629356620
> 240        M      WRN -4.148942985
> 241        S      WRN -1.855994142
> 242        R      WT1 -0.824982393
> 243        S      WT1  1.236129501
> 244        S      WT1  1.088540877
>
>         [[alternative HTML version deleted]]
>
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