1311 lines
61 KiB
TeX
1311 lines
61 KiB
TeX
% Options for packages loaded elsewhere
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\hypersetup{
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pdftitle={Projet},
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hidelinks,
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pdfcreator={LaTeX via pandoc}}
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\title{Projet}
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\author{}
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\date{\vspace{-2.5em}2024-12-04}
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\begin{document}
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\maketitle
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\begin{Shaded}
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\begin{Highlighting}[]
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\NormalTok{T }\OtherTok{=} \FunctionTok{read.table}\NormalTok{(}\StringTok{"DataProjet3MIC{-}2425.txt"}\NormalTok{,}\AttributeTok{header=}\ConstantTok{TRUE}\NormalTok{,}\AttributeTok{sep=}\StringTok{";"}\NormalTok{)}
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\NormalTok{T}\SpecialCharTok{$}\NormalTok{ExpT1 }\OtherTok{=} \FunctionTok{as.factor}\NormalTok{(T}\SpecialCharTok{$}\NormalTok{ExpT1)}
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\FunctionTok{head}\NormalTok{(T)}
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\end{Highlighting}
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\end{Shaded}
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\begin{verbatim}
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## T1_1H_R1 T1_2H_R1 T1_3H_R1 T1_4H_R1 T1_5H_R1 T1_6H_R1
|
||
## G5 -0.2054734 -0.6888206 -0.18108429 -0.066565379 0.52170865 0.4480939
|
||
## G6 -0.6195103 -0.8561376 -0.02108391 -0.144561565 0.49344924 0.4536955
|
||
## G11 0.3087073 0.8172262 -0.56147370 0.181479326 -0.33704562 -0.3731662
|
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## G13 0.1924929 0.1476873 0.24238730 0.561824906 0.04531418 -0.6351644
|
||
## G18 0.1080725 0.2881167 -0.19747270 -0.001549827 -0.22740847 -0.5709062
|
||
## G23 0.1135094 -0.2969878 -0.13434839 0.071241947 -0.59324439 0.7029352
|
||
## T2_1H_R1 T2_2H_R1 T2_3H_R1 T2_4H_R1 T2_5H_R1 T2_6H_R1
|
||
## G5 -0.4491395 -1.51438243 -3.8153763 -2.5030107 -2.91443708 -3.572760
|
||
## G6 -0.5715679 -1.47552917 -3.0786353 -2.2175271 -2.26586463 -3.359180
|
||
## G11 -0.2089430 -1.28998670 -2.6332288 -2.4010825 -2.43974374 -2.033578
|
||
## G13 0.5262851 1.43148420 1.8420478 1.8328251 1.92424716 2.192265
|
||
## G18 0.3401306 -0.04682641 -0.3267337 -0.4701502 0.01529052 2.167138
|
||
## G23 0.1681757 -1.33944054 -2.8555289 -3.4466995 -4.29654702 -3.843560
|
||
## T3_1H_R1 T3_2H_R1 T3_3H_R1 T3_4H_R1 T3_5H_R1 T3_6H_R1
|
||
## G5 -0.66446988 -2.522064 -1.7969866 -2.967056 -2.991815880 -2.836828
|
||
## G6 -0.54270432 -2.281383 -1.5971483 -2.635147 -2.424743983 -2.535588
|
||
## G11 -0.27086062 -1.176080 -3.0179239 -2.952781 -2.963556862 -2.490674
|
||
## G13 0.41267413 1.687565 1.8118555 1.867925 2.142488325 2.098050
|
||
## G18 -0.04019622 0.179040 -0.1922123 -0.552894 -0.005530098 2.092308
|
||
## G23 0.55921015 -1.338337 -2.6151952 -3.555361 -4.375187079 -3.605193
|
||
## T1_1H_R2 T1_2H_R2 T1_3H_R2 T1_4H_R2 T1_5H_R2 T1_6H_R2
|
||
## G5 -0.2499091 -0.237592463 -0.7414745 0.5043795 0.3548600 0.6983094
|
||
## G6 -0.5265623 -0.347359147 -0.6399105 0.2740703 0.3466837 0.6626021
|
||
## G11 0.3029732 0.547722402 0.5885428 -0.9077323 -1.4279824 -0.6993109
|
||
## G13 -0.2344408 -0.289916318 0.7250230 -0.4877646 -0.2893664 -0.6486218
|
||
## G18 -0.3295655 0.004397478 0.1714382 -0.5300958 -0.4808025 -0.7135995
|
||
## G23 -0.1475303 -0.044008927 -0.4404662 0.1751426 -0.4610258 0.7436764
|
||
## T2_1H_R2 T2_2H_R2 T2_3H_R2 T2_4H_R2 T2_5H_R2 T2_6H_R2 T3_1H_R2
|
||
## G5 -0.6705182 -2.4890394 -2.398936 -2.5517659 -2.4744365 -3.144543 -0.6195184
|
||
## G6 -0.6704720 -2.4162352 -2.209975 -2.1976128 -2.2384780 -2.468120 -0.8422885
|
||
## G11 0.1630917 -2.3067461 -2.320666 -3.2938063 -2.9668778 -3.183063 -0.1946611
|
||
## G13 0.2720468 1.4695457 1.831608 1.6181355 2.1912834 2.188585 0.1704330
|
||
## G18 -0.3731123 -0.1094265 0.130255 -0.4527278 0.8875215 2.180169 -0.4460246
|
||
## G23 -0.1353737 -1.4500180 -2.235124 -3.7803063 -4.1084129 -4.471728 -0.2753172
|
||
## T3_2H_R2 T3_3H_R2 T3_4H_R2 T3_5H_R2 T3_6H_R2 ExpT1 ExpT2 ExpT3
|
||
## G5 -2.7064195 -2.8284978 -2.8493415 -2.938259 -3.390693 Non Sous Sous
|
||
## G6 -2.4478142 -2.5524222 -2.4837090 -2.461097 -2.970514 Non Sous Sous
|
||
## G11 -2.1067567 -2.6235631 -3.0237474 -2.807225 -2.698180 Non Sous Sous
|
||
## G13 1.5124230 2.0506932 1.5586937 2.317673 2.156185 Non Sur Sur
|
||
## G18 0.0383623 -0.1107769 -0.2219528 1.187512 1.952405 Non Sur Sur
|
||
## G23 -1.4062330 -2.2049955 -3.1804119 -3.940839 -4.668680 Non Sous Sous
|
||
\end{verbatim}
|
||
|
||
\begin{Shaded}
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\begin{Highlighting}[]
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\FunctionTok{summary}\NormalTok{(T)}
|
||
\end{Highlighting}
|
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\end{Shaded}
|
||
|
||
\begin{verbatim}
|
||
## T1_1H_R1 T1_2H_R1 T1_3H_R1 T1_4H_R1
|
||
## Min. :-3.58436 Min. :-4.3034 Min. :-2.26607 Min. :-2.56731
|
||
## 1st Qu.:-0.22978 1st Qu.:-0.1404 1st Qu.:-0.28249 1st Qu.:-0.42895
|
||
## Median :-0.03631 Median : 0.1420 Median :-0.05927 Median : 0.16867
|
||
## Mean :-0.02951 Mean : 0.1767 Mean : 0.04103 Mean : 0.05281
|
||
## 3rd Qu.: 0.12204 3rd Qu.: 0.3904 3rd Qu.: 0.15839 3rd Qu.: 0.44483
|
||
## Max. : 5.06654 Max. : 7.2821 Max. : 6.61788 Max. : 6.87671
|
||
## T1_5H_R1 T1_6H_R1 T2_1H_R1 T2_2H_R1
|
||
## Min. :-5.5106 Min. :-2.9759 Min. :-4.30401 Min. :-4.5825
|
||
## 1st Qu.:-0.4788 1st Qu.:-0.6124 1st Qu.:-0.43935 1st Qu.:-0.9932
|
||
## Median :-0.1984 Median :-0.3724 Median : 0.13065 Median : 0.3289
|
||
## Mean :-0.1585 Mean :-0.2416 Mean : 0.06039 Mean : 0.4714
|
||
## 3rd Qu.: 0.2077 3rd Qu.: 0.2413 3rd Qu.: 0.46011 3rd Qu.: 1.9464
|
||
## Max. : 5.8582 Max. : 4.1009 Max. : 8.66345 Max. : 8.7483
|
||
## T2_3H_R1 T2_4H_R1 T2_5H_R1 T2_6H_R1
|
||
## Min. :-6.6293 Min. :-5.813548 Min. :-5.8017 Min. :-5.6784
|
||
## 1st Qu.:-2.0451 1st Qu.:-2.406108 1st Qu.:-2.4172 1st Qu.:-2.5552
|
||
## Median : 0.3733 Median : 0.008421 Median : 0.7556 Median : 1.8857
|
||
## Mean : 0.3805 Mean : 0.197409 Mean : 0.1521 Mean : 0.2313
|
||
## 3rd Qu.: 2.7644 3rd Qu.: 2.699218 3rd Qu.: 2.5236 3rd Qu.: 2.7235
|
||
## Max. : 8.9881 Max. : 7.503939 Max. : 7.0606 Max. : 8.8815
|
||
## T3_1H_R1 T3_2H_R1 T3_3H_R1 T3_4H_R1
|
||
## Min. :-2.9561 Min. :-4.9884 Min. :-5.8280 Min. :-6.0789
|
||
## 1st Qu.:-0.4409 1st Qu.:-1.1066 1st Qu.:-1.5925 1st Qu.:-2.4930
|
||
## Median : 0.1573 Median : 0.6914 Median : 0.9585 Median : 0.9982
|
||
## Mean : 0.1714 Mean : 0.5878 Mean : 0.6387 Mean : 0.2736
|
||
## 3rd Qu.: 0.6673 3rd Qu.: 2.3016 3rd Qu.: 2.7533 3rd Qu.: 2.7854
|
||
## Max. : 8.6849 Max. : 8.6560 Max. : 8.0950 Max. : 7.0103
|
||
## T3_5H_R1 T3_6H_R1 T1_1H_R2 T1_2H_R2
|
||
## Min. :-6.910 Min. :-4.7625 Min. :-2.11580 Min. :-2.75004
|
||
## 1st Qu.:-2.487 1st Qu.:-2.0911 1st Qu.:-0.28225 1st Qu.:-0.27271
|
||
## Median : 1.156 Median : 1.8690 Median :-0.02432 Median :-0.04075
|
||
## Mean : 0.258 Mean : 0.3913 Mean :-0.04445 Mean : 0.10717
|
||
## 3rd Qu.: 2.709 3rd Qu.: 2.4879 3rd Qu.: 0.15670 3rd Qu.: 0.25383
|
||
## Max. : 6.529 Max. : 8.6398 Max. : 4.70943 Max. : 7.03638
|
||
## T1_3H_R2 T1_4H_R2 T1_5H_R2 T1_6H_R2
|
||
## Min. :-3.2539 Min. :-3.50770 Min. :-3.3307 Min. :-2.4863
|
||
## 1st Qu.:-0.1229 1st Qu.:-0.51001 1st Qu.:-0.6437 1st Qu.:-0.9686
|
||
## Median : 0.2674 Median :-0.27091 Median :-0.3845 Median :-0.7215
|
||
## Mean : 0.3033 Mean :-0.02457 Mean :-0.2410 Mean :-0.3082
|
||
## 3rd Qu.: 0.5068 3rd Qu.: 0.27652 3rd Qu.: 0.1442 3rd Qu.: 0.5814
|
||
## Max. : 7.1995 Max. : 6.52284 Max. : 5.2469 Max. : 3.9054
|
||
## T2_1H_R2 T2_2H_R2 T2_3H_R2 T2_4H_R2
|
||
## Min. :-2.38587 Min. :-5.8266 Min. :-4.6135 Min. :-6.4553
|
||
## 1st Qu.:-0.48477 1st Qu.:-1.2309 1st Qu.:-1.4511 1st Qu.:-2.3416
|
||
## Median : 0.03105 Median : 0.6644 Median : 0.5351 Median : 0.5323
|
||
## Mean : 0.08932 Mean : 0.4684 Mean : 0.5999 Mean : 0.1279
|
||
## 3rd Qu.: 0.61495 3rd Qu.: 2.1298 3rd Qu.: 2.5954 3rd Qu.: 2.4618
|
||
## Max. : 8.59820 Max. : 8.8928 Max. : 8.4956 Max. : 8.0010
|
||
## T2_5H_R2 T2_6H_R2 T3_1H_R2 T3_2H_R2
|
||
## Min. :-6.1685 Min. :-6.2234 Min. :-3.22436 Min. :-6.0944
|
||
## 1st Qu.:-2.4058 1st Qu.:-2.6251 1st Qu.:-0.61705 1st Qu.:-1.3567
|
||
## Median : 1.0892 Median : 2.0014 Median : 0.07589 Median : 0.7670
|
||
## Mean : 0.1411 Mean : 0.1572 Mean : 0.11618 Mean : 0.5725
|
||
## 3rd Qu.: 2.5033 3rd Qu.: 2.5375 3rd Qu.: 0.76673 3rd Qu.: 2.3150
|
||
## Max. : 7.4521 Max. : 8.7777 Max. : 8.77729 Max. : 8.6354
|
||
## T3_3H_R2 T3_4H_R2 T3_5H_R2 T3_6H_R2
|
||
## Min. :-6.0135 Min. :-6.0345 Min. :-6.8294 Min. :-7.24672
|
||
## 1st Qu.:-1.8079 1st Qu.:-2.2277 1st Qu.:-2.5646 1st Qu.:-2.80051
|
||
## Median : 1.1183 Median : 1.1769 Median : 1.6539 Median : 1.92082
|
||
## Mean : 0.5828 Mean : 0.3157 Mean : 0.1338 Mean : 0.05484
|
||
## 3rd Qu.: 2.8892 3rd Qu.: 2.6455 3rd Qu.: 2.5664 3rd Qu.: 2.46450
|
||
## Max. : 8.2637 Max. : 7.4777 Max. : 6.9137 Max. : 8.69285
|
||
## ExpT1 ExpT2 ExpT3
|
||
## Non :441 Non : 11 Non : 7
|
||
## Sous: 57 Sous:247 Sous:247
|
||
## Sur : 44 Sur :284 Sur :288
|
||
##
|
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##
|
||
##
|
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\end{verbatim}
|
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|
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\begin{Shaded}
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\begin{Highlighting}[]
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\FunctionTok{str}\NormalTok{(T)}
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\end{Highlighting}
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\end{Shaded}
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|
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\begin{verbatim}
|
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## 'data.frame': 542 obs. of 39 variables:
|
||
## $ T1_1H_R1: num -0.205 -0.62 0.309 0.192 0.108 ...
|
||
## $ T1_2H_R1: num -0.689 -0.856 0.817 0.148 0.288 ...
|
||
## $ T1_3H_R1: num -0.1811 -0.0211 -0.5615 0.2424 -0.1975 ...
|
||
## $ T1_4H_R1: num -0.06657 -0.14456 0.18148 0.56182 -0.00155 ...
|
||
## $ T1_5H_R1: num 0.5217 0.4934 -0.337 0.0453 -0.2274 ...
|
||
## $ T1_6H_R1: num 0.448 0.454 -0.373 -0.635 -0.571 ...
|
||
## $ T2_1H_R1: num -0.449 -0.572 -0.209 0.526 0.34 ...
|
||
## $ T2_2H_R1: num -1.5144 -1.4755 -1.29 1.4315 -0.0468 ...
|
||
## $ T2_3H_R1: num -3.815 -3.079 -2.633 1.842 -0.327 ...
|
||
## $ T2_4H_R1: num -2.5 -2.22 -2.4 1.83 -0.47 ...
|
||
## $ T2_5H_R1: num -2.9144 -2.2659 -2.4397 1.9242 0.0153 ...
|
||
## $ T2_6H_R1: num -3.57 -3.36 -2.03 2.19 2.17 ...
|
||
## $ T3_1H_R1: num -0.6645 -0.5427 -0.2709 0.4127 -0.0402 ...
|
||
## $ T3_2H_R1: num -2.522 -2.281 -1.176 1.688 0.179 ...
|
||
## $ T3_3H_R1: num -1.797 -1.597 -3.018 1.812 -0.192 ...
|
||
## $ T3_4H_R1: num -2.967 -2.635 -2.953 1.868 -0.553 ...
|
||
## $ T3_5H_R1: num -2.99182 -2.42474 -2.96356 2.14249 -0.00553 ...
|
||
## $ T3_6H_R1: num -2.84 -2.54 -2.49 2.1 2.09 ...
|
||
## $ T1_1H_R2: num -0.25 -0.527 0.303 -0.234 -0.33 ...
|
||
## $ T1_2H_R2: num -0.2376 -0.3474 0.5477 -0.2899 0.0044 ...
|
||
## $ T1_3H_R2: num -0.741 -0.64 0.589 0.725 0.171 ...
|
||
## $ T1_4H_R2: num 0.504 0.274 -0.908 -0.488 -0.53 ...
|
||
## $ T1_5H_R2: num 0.355 0.347 -1.428 -0.289 -0.481 ...
|
||
## $ T1_6H_R2: num 0.698 0.663 -0.699 -0.649 -0.714 ...
|
||
## $ T2_1H_R2: num -0.671 -0.67 0.163 0.272 -0.373 ...
|
||
## $ T2_2H_R2: num -2.489 -2.416 -2.307 1.47 -0.109 ...
|
||
## $ T2_3H_R2: num -2.4 -2.21 -2.32 1.83 0.13 ...
|
||
## $ T2_4H_R2: num -2.552 -2.198 -3.294 1.618 -0.453 ...
|
||
## $ T2_5H_R2: num -2.474 -2.238 -2.967 2.191 0.888 ...
|
||
## $ T2_6H_R2: num -3.14 -2.47 -3.18 2.19 2.18 ...
|
||
## $ T3_1H_R2: num -0.62 -0.842 -0.195 0.17 -0.446 ...
|
||
## $ T3_2H_R2: num -2.7064 -2.4478 -2.1068 1.5124 0.0384 ...
|
||
## $ T3_3H_R2: num -2.828 -2.552 -2.624 2.051 -0.111 ...
|
||
## $ T3_4H_R2: num -2.849 -2.484 -3.024 1.559 -0.222 ...
|
||
## $ T3_5H_R2: num -2.94 -2.46 -2.81 2.32 1.19 ...
|
||
## $ T3_6H_R2: num -3.39 -2.97 -2.7 2.16 1.95 ...
|
||
## $ ExpT1 : Factor w/ 3 levels "Non","Sous","Sur": 1 1 1 1 1 1 1 1 1 1 ...
|
||
## $ ExpT2 : Factor w/ 3 levels "Non","Sous","Sur": 2 2 2 3 3 2 3 3 2 2 ...
|
||
## $ ExpT3 : Factor w/ 3 levels "Non","Sous","Sur": 2 2 2 3 3 2 3 3 2 2 ...
|
||
\end{verbatim}
|
||
|
||
\begin{Shaded}
|
||
\begin{Highlighting}[]
|
||
\FunctionTok{levels}\NormalTok{(T}\SpecialCharTok{$}\NormalTok{ExpT1)}
|
||
\end{Highlighting}
|
||
\end{Shaded}
|
||
|
||
\begin{verbatim}
|
||
## [1] "Non" "Sous" "Sur"
|
||
\end{verbatim}
|
||
|
||
\subsubsection{Contenu du jeu de données
|
||
:}\label{contenu-du-jeu-de-donnuxe9es}
|
||
|
||
\begin{itemize}
|
||
\item
|
||
3 variables qualitatives nominales représentant l'expression du gêne
|
||
\[g\] dont les modalités sont \[\{"sur","sous","non"\}\]. chaque
|
||
variable correspond respectivement à la différence d'expression du
|
||
gêne mesurée à la 6èeme heure lors du traitement
|
||
\[T \in \{T1,T2,T3\}\]
|
||
\item
|
||
\[3*6 + 3*6 = 36\] variables quantitatives continues représentant les
|
||
effets des traitements sur l'expression des gênes T1 T2 et T3 à
|
||
1h,2h,3h,4h,5h,6h après l'administration pour les replicats R1 et R2,
|
||
par rapport à leur expression à T=0 ( sans traitement).
|
||
\item
|
||
Ce jeu de données contient des relevés sur 542 individus, ici des
|
||
gênes.
|
||
\end{itemize}
|
||
|
||
\subsection{Analyse unidimentionnelle
|
||
:}\label{analyse-unidimentionnelle}
|
||
|
||
\subsubsection{Expression des gênes lors du traitement
|
||
T1}\label{expression-des-guxeanes-lors-du-traitement-t1}
|
||
|
||
\begin{Shaded}
|
||
\begin{Highlighting}[]
|
||
\NormalTok{g1}\OtherTok{\textless{}{-}}\FunctionTok{ggplot}\NormalTok{(T, }\FunctionTok{aes}\NormalTok{(}\AttributeTok{x=}\NormalTok{T}\SpecialCharTok{$}\NormalTok{ExpT1))}\SpecialCharTok{+}
|
||
\FunctionTok{geom\_bar}\NormalTok{()}\SpecialCharTok{+}
|
||
\FunctionTok{ylab}\NormalTok{(}\StringTok{"Effectifs"}\NormalTok{)}\SpecialCharTok{+}\FunctionTok{ggtitle}\NormalTok{(}\StringTok{"Effectifs"}\NormalTok{)}
|
||
\NormalTok{g2}\OtherTok{\textless{}{-}}\FunctionTok{ggplot}\NormalTok{(T, }\FunctionTok{aes}\NormalTok{(}\AttributeTok{x =}\NormalTok{ T}\SpecialCharTok{$}\NormalTok{ExpT1)) }\SpecialCharTok{+}
|
||
\FunctionTok{geom\_bar}\NormalTok{(}\FunctionTok{aes}\NormalTok{(}\AttributeTok{y =}\NormalTok{ (..count..)}\SpecialCharTok{/}\FunctionTok{sum}\NormalTok{(..count..)))}\SpecialCharTok{+}\FunctionTok{ylab}\NormalTok{(}\StringTok{""}\NormalTok{)}\SpecialCharTok{+}\FunctionTok{ggtitle}\NormalTok{(}\StringTok{"Frequences"}\NormalTok{)}
|
||
|
||
\NormalTok{df }\OtherTok{\textless{}{-}} \FunctionTok{data.frame}\NormalTok{(}\AttributeTok{group =} \FunctionTok{levels}\NormalTok{(T}\SpecialCharTok{$}\NormalTok{ExpT1),}
|
||
\AttributeTok{value =} \FunctionTok{as.vector}\NormalTok{(}\FunctionTok{table}\NormalTok{(T}\SpecialCharTok{$}\NormalTok{ExpT1))}\SpecialCharTok{/}\FunctionTok{nrow}\NormalTok{(T))}
|
||
\NormalTok{g3}\OtherTok{\textless{}{-}}\FunctionTok{ggplot}\NormalTok{(df, }\FunctionTok{aes}\NormalTok{(}\AttributeTok{x=}\StringTok{""}\NormalTok{, }\AttributeTok{y=}\NormalTok{value, }\AttributeTok{fill=}\NormalTok{group))}\SpecialCharTok{+}
|
||
\FunctionTok{geom\_bar}\NormalTok{(}\AttributeTok{width =} \DecValTok{1}\NormalTok{, }\AttributeTok{stat =} \StringTok{"identity"}\NormalTok{)}\SpecialCharTok{+}
|
||
\FunctionTok{coord\_polar}\NormalTok{(}\StringTok{"y"}\NormalTok{, }\AttributeTok{start=}\DecValTok{0}\NormalTok{)}\SpecialCharTok{+}
|
||
\FunctionTok{theme}\NormalTok{(}\AttributeTok{legend.position=}\StringTok{"bottom"}\NormalTok{)}
|
||
\FunctionTok{grid.arrange}\NormalTok{(g3,g1,g2,}\AttributeTok{ncol=}\DecValTok{3}\NormalTok{)}
|
||
\end{Highlighting}
|
||
\end{Shaded}
|
||
|
||
\begin{verbatim}
|
||
## Warning: Use of `T$ExpT1` is discouraged.
|
||
## i Use `ExpT1` instead.
|
||
\end{verbatim}
|
||
|
||
\begin{verbatim}
|
||
## Warning: The dot-dot notation (`..count..`) was deprecated in ggplot2 3.4.0.
|
||
## i Please use `after_stat(count)` instead.
|
||
## This warning is displayed once every 8 hours.
|
||
## Call `lifecycle::last_lifecycle_warnings()` to see where this warning was
|
||
## generated.
|
||
\end{verbatim}
|
||
|
||
\begin{verbatim}
|
||
## Warning: Use of `T$ExpT1` is discouraged.
|
||
## i Use `ExpT1` instead.
|
||
\end{verbatim}
|
||
|
||
\includegraphics{Projet_files/figure-latex/unnamed-chunk-2-1.pdf}
|
||
|
||
\subsubsection{Expression des gênes lors du traitement
|
||
T2}\label{expression-des-guxeanes-lors-du-traitement-t2}
|
||
|
||
\begin{Shaded}
|
||
\begin{Highlighting}[]
|
||
\NormalTok{g1}\OtherTok{\textless{}{-}}\FunctionTok{ggplot}\NormalTok{(T, }\FunctionTok{aes}\NormalTok{(}\AttributeTok{x=}\NormalTok{T}\SpecialCharTok{$}\NormalTok{ExpT2))}\SpecialCharTok{+}
|
||
\FunctionTok{geom\_bar}\NormalTok{()}\SpecialCharTok{+}
|
||
\FunctionTok{ylab}\NormalTok{(}\StringTok{"Effectifs"}\NormalTok{)}\SpecialCharTok{+}\FunctionTok{ggtitle}\NormalTok{(}\StringTok{"Effectifs"}\NormalTok{)}
|
||
\NormalTok{g2}\OtherTok{\textless{}{-}}\FunctionTok{ggplot}\NormalTok{(T, }\FunctionTok{aes}\NormalTok{(}\AttributeTok{x =}\NormalTok{ T}\SpecialCharTok{$}\NormalTok{ExpT2)) }\SpecialCharTok{+}
|
||
\FunctionTok{geom\_bar}\NormalTok{(}\FunctionTok{aes}\NormalTok{(}\AttributeTok{y =}\NormalTok{ (..count..)}\SpecialCharTok{/}\FunctionTok{sum}\NormalTok{(..count..)))}\SpecialCharTok{+}\FunctionTok{ylab}\NormalTok{(}\StringTok{""}\NormalTok{)}\SpecialCharTok{+}\FunctionTok{ggtitle}\NormalTok{(}\StringTok{"Frequences"}\NormalTok{)}
|
||
|
||
\NormalTok{df }\OtherTok{\textless{}{-}} \FunctionTok{data.frame}\NormalTok{(}\AttributeTok{group =} \FunctionTok{levels}\NormalTok{(T}\SpecialCharTok{$}\NormalTok{ExpT2),}
|
||
\AttributeTok{value =} \FunctionTok{as.vector}\NormalTok{(}\FunctionTok{table}\NormalTok{(T}\SpecialCharTok{$}\NormalTok{ExpT2))}\SpecialCharTok{/}\FunctionTok{nrow}\NormalTok{(T))}
|
||
\NormalTok{g3}\OtherTok{\textless{}{-}}\FunctionTok{ggplot}\NormalTok{(df, }\FunctionTok{aes}\NormalTok{(}\AttributeTok{x=}\StringTok{""}\NormalTok{, }\AttributeTok{y=}\NormalTok{value, }\AttributeTok{fill=}\NormalTok{group))}\SpecialCharTok{+}
|
||
\FunctionTok{geom\_bar}\NormalTok{(}\AttributeTok{width =} \DecValTok{1}\NormalTok{, }\AttributeTok{stat =} \StringTok{"identity"}\NormalTok{)}\SpecialCharTok{+}
|
||
\FunctionTok{coord\_polar}\NormalTok{(}\StringTok{"y"}\NormalTok{, }\AttributeTok{start=}\DecValTok{0}\NormalTok{)}\SpecialCharTok{+}
|
||
\FunctionTok{theme}\NormalTok{(}\AttributeTok{legend.position=}\StringTok{"bottom"}\NormalTok{)}
|
||
\FunctionTok{grid.arrange}\NormalTok{(g3,g1,g2,}\AttributeTok{ncol=}\DecValTok{3}\NormalTok{)}
|
||
\end{Highlighting}
|
||
\end{Shaded}
|
||
|
||
\begin{verbatim}
|
||
## Warning: Use of `T$ExpT2` is discouraged.
|
||
## i Use `ExpT2` instead.
|
||
## Use of `T$ExpT2` is discouraged.
|
||
## i Use `ExpT2` instead.
|
||
\end{verbatim}
|
||
|
||
\includegraphics{Projet_files/figure-latex/unnamed-chunk-3-1.pdf}
|
||
|
||
\subsubsection{Expression des gênes lors du traitement
|
||
T3}\label{expression-des-guxeanes-lors-du-traitement-t3}
|
||
|
||
\begin{Shaded}
|
||
\begin{Highlighting}[]
|
||
\NormalTok{g1}\OtherTok{\textless{}{-}}\FunctionTok{ggplot}\NormalTok{(T, }\FunctionTok{aes}\NormalTok{(}\AttributeTok{x=}\NormalTok{T}\SpecialCharTok{$}\NormalTok{ExpT3))}\SpecialCharTok{+}
|
||
\FunctionTok{geom\_bar}\NormalTok{()}\SpecialCharTok{+}
|
||
\FunctionTok{ylab}\NormalTok{(}\StringTok{"Effectifs"}\NormalTok{)}\SpecialCharTok{+}\FunctionTok{ggtitle}\NormalTok{(}\StringTok{"Effectifs"}\NormalTok{)}
|
||
\NormalTok{g2}\OtherTok{\textless{}{-}}\FunctionTok{ggplot}\NormalTok{(T, }\FunctionTok{aes}\NormalTok{(}\AttributeTok{x =}\NormalTok{ T}\SpecialCharTok{$}\NormalTok{ExpT3)) }\SpecialCharTok{+}
|
||
\FunctionTok{geom\_bar}\NormalTok{(}\FunctionTok{aes}\NormalTok{(}\AttributeTok{y =}\NormalTok{ (..count..)}\SpecialCharTok{/}\FunctionTok{sum}\NormalTok{(..count..)))}\SpecialCharTok{+}\FunctionTok{ylab}\NormalTok{(}\StringTok{""}\NormalTok{)}\SpecialCharTok{+}\FunctionTok{ggtitle}\NormalTok{(}\StringTok{"Frequences"}\NormalTok{)}
|
||
|
||
\NormalTok{df }\OtherTok{\textless{}{-}} \FunctionTok{data.frame}\NormalTok{(}\AttributeTok{group =} \FunctionTok{levels}\NormalTok{(T}\SpecialCharTok{$}\NormalTok{ExpT3),}
|
||
\AttributeTok{value =} \FunctionTok{as.vector}\NormalTok{(}\FunctionTok{table}\NormalTok{(T}\SpecialCharTok{$}\NormalTok{ExpT3))}\SpecialCharTok{/}\FunctionTok{nrow}\NormalTok{(T))}
|
||
\NormalTok{g3}\OtherTok{\textless{}{-}}\FunctionTok{ggplot}\NormalTok{(df, }\FunctionTok{aes}\NormalTok{(}\AttributeTok{x=}\StringTok{""}\NormalTok{, }\AttributeTok{y=}\NormalTok{value, }\AttributeTok{fill=}\NormalTok{group))}\SpecialCharTok{+}
|
||
\FunctionTok{geom\_bar}\NormalTok{(}\AttributeTok{width =} \DecValTok{1}\NormalTok{, }\AttributeTok{stat =} \StringTok{"identity"}\NormalTok{)}\SpecialCharTok{+}
|
||
\FunctionTok{coord\_polar}\NormalTok{(}\StringTok{"y"}\NormalTok{, }\AttributeTok{start=}\DecValTok{0}\NormalTok{)}\SpecialCharTok{+}
|
||
\FunctionTok{theme}\NormalTok{(}\AttributeTok{legend.position=}\StringTok{"bottom"}\NormalTok{)}
|
||
\FunctionTok{grid.arrange}\NormalTok{(g3,g1,g2,}\AttributeTok{ncol=}\DecValTok{3}\NormalTok{)}
|
||
\end{Highlighting}
|
||
\end{Shaded}
|
||
|
||
\begin{verbatim}
|
||
## Warning: Use of `T$ExpT3` is discouraged.
|
||
## i Use `ExpT3` instead.
|
||
## Use of `T$ExpT3` is discouraged.
|
||
## i Use `ExpT3` instead.
|
||
\end{verbatim}
|
||
|
||
\includegraphics{Projet_files/figure-latex/unnamed-chunk-4-1.pdf}
|
||
|
||
\subsubsection{Analyse de de ces 3
|
||
variables}\label{analyse-de-de-ces-3-variables}
|
||
|
||
On remarque que les traitements T2 et T3 semblent avoir un effet assez
|
||
similaire sur l'expression des gênes relevée à la 6ème heure : Une
|
||
polarisation entre la sous expression et la sur expression qui se
|
||
partagent presque la totalité des relevés, avec un poids légèrement
|
||
superieur à 55\% pour la sur-expression au détriment de la
|
||
sous-expression. Cela a peut être un rapporrt avec le fait que T3 est
|
||
une combinaison des traitement T1 et T2.
|
||
|
||
T1 quant à lui se démarque grandement par une large majorité (Un peu
|
||
plus de 80\%), de gêne n'ayant pas changé d'expression après 6h de
|
||
traitement.
|
||
|
||
\subsubsection{Expression relative des gênes mesurées à intervalle
|
||
régulier}\label{expression-relative-des-guxeanes-mesuruxe9es-uxe0-intervalle-ruxe9gulier}
|
||
|
||
\paragraph{Traitement T1}\label{traitement-t1}
|
||
|
||
\begin{Shaded}
|
||
\begin{Highlighting}[]
|
||
\CommentTok{\#apply(T[{-}c(37:39)],2,function(col)\{}
|
||
\CommentTok{\# which(T == col)}
|
||
\CommentTok{\#hist(col, main = paste("Histogram of", colnames(T)[which(T == col)[2]]),}
|
||
\CommentTok{\# xlab = "Values", col = "lightblue", border = "black")}
|
||
\CommentTok{\#\})}
|
||
\NormalTok{T\_long }\OtherTok{=} \FunctionTok{melt}\NormalTok{(T[}\FunctionTok{c}\NormalTok{(}\DecValTok{1}\NormalTok{,}\DecValTok{2}\NormalTok{,}\DecValTok{3}\NormalTok{,}\DecValTok{4}\NormalTok{,}\DecValTok{5}\NormalTok{,}\DecValTok{6}\NormalTok{,}\DecValTok{19}\NormalTok{,}\DecValTok{20}\NormalTok{,}\DecValTok{21}\NormalTok{,}\DecValTok{22}\NormalTok{,}\DecValTok{23}\NormalTok{,}\DecValTok{24}\NormalTok{)])}
|
||
\end{Highlighting}
|
||
\end{Shaded}
|
||
|
||
\begin{verbatim}
|
||
## No id variables; using all as measure variables
|
||
\end{verbatim}
|
||
|
||
\begin{Shaded}
|
||
\begin{Highlighting}[]
|
||
\FunctionTok{ggplot}\NormalTok{(T\_long, }\FunctionTok{aes}\NormalTok{(}\AttributeTok{x =}\NormalTok{ value)) }\SpecialCharTok{+}
|
||
\FunctionTok{geom\_histogram}\NormalTok{(}\AttributeTok{binwidth =} \DecValTok{1}\NormalTok{, }\AttributeTok{fill =} \StringTok{"blue"}\NormalTok{, }\AttributeTok{color =} \StringTok{"black"}\NormalTok{, }\AttributeTok{alpha =} \FloatTok{0.7}\NormalTok{) }\SpecialCharTok{+}
|
||
\FunctionTok{facet\_wrap}\NormalTok{(}\SpecialCharTok{\textasciitilde{}}\NormalTok{variable,}\AttributeTok{scales =} \StringTok{"free"}\NormalTok{,}\AttributeTok{ncol=}\DecValTok{6}\NormalTok{) }\SpecialCharTok{+}
|
||
\FunctionTok{labs}\NormalTok{(}\AttributeTok{title =} \StringTok{"Histograms for Each Column"}\NormalTok{, }\AttributeTok{x =} \StringTok{"Values"}\NormalTok{, }\AttributeTok{y =} \StringTok{"Frequency"}\NormalTok{)}
|
||
\end{Highlighting}
|
||
\end{Shaded}
|
||
|
||
\includegraphics{Projet_files/figure-latex/unnamed-chunk-5-1.pdf} \#\#\#
|
||
Traitement T2
|
||
|
||
\begin{Shaded}
|
||
\begin{Highlighting}[]
|
||
\NormalTok{T\_long }\OtherTok{=} \FunctionTok{melt}\NormalTok{(T[}\FunctionTok{c}\NormalTok{(}\DecValTok{7}\NormalTok{,}\DecValTok{8}\NormalTok{,}\DecValTok{9}\NormalTok{,}\DecValTok{10}\NormalTok{,}\DecValTok{11}\NormalTok{,}\DecValTok{12}\NormalTok{,}\DecValTok{25}\NormalTok{,}\DecValTok{26}\NormalTok{,}\DecValTok{27}\NormalTok{,}\DecValTok{28}\NormalTok{,}\DecValTok{29}\NormalTok{,}\DecValTok{30}\NormalTok{)])}
|
||
\end{Highlighting}
|
||
\end{Shaded}
|
||
|
||
\begin{verbatim}
|
||
## No id variables; using all as measure variables
|
||
\end{verbatim}
|
||
|
||
\begin{Shaded}
|
||
\begin{Highlighting}[]
|
||
\FunctionTok{ggplot}\NormalTok{(T\_long, }\FunctionTok{aes}\NormalTok{(}\AttributeTok{x =}\NormalTok{ value)) }\SpecialCharTok{+}
|
||
\FunctionTok{geom\_histogram}\NormalTok{(}\AttributeTok{binwidth =} \DecValTok{1}\NormalTok{, }\AttributeTok{fill =} \StringTok{"blue"}\NormalTok{, }\AttributeTok{color =} \StringTok{"black"}\NormalTok{, }\AttributeTok{alpha =} \FloatTok{0.7}\NormalTok{) }\SpecialCharTok{+}
|
||
\FunctionTok{facet\_wrap}\NormalTok{(}\SpecialCharTok{\textasciitilde{}}\NormalTok{variable,}\AttributeTok{scales =} \StringTok{"free"}\NormalTok{,}\AttributeTok{ncol=}\DecValTok{6}\NormalTok{) }\SpecialCharTok{+}
|
||
\FunctionTok{labs}\NormalTok{(}\AttributeTok{title =} \StringTok{"Histograms for Each Column"}\NormalTok{, }\AttributeTok{x =} \StringTok{"Values"}\NormalTok{, }\AttributeTok{y =} \StringTok{"Frequency"}\NormalTok{)}
|
||
\end{Highlighting}
|
||
\end{Shaded}
|
||
|
||
\includegraphics{Projet_files/figure-latex/unnamed-chunk-6-1.pdf} \#\#\#
|
||
Traitement T3
|
||
|
||
\begin{Shaded}
|
||
\begin{Highlighting}[]
|
||
\NormalTok{T\_long }\OtherTok{=} \FunctionTok{melt}\NormalTok{(T[}\FunctionTok{c}\NormalTok{(}\DecValTok{13}\NormalTok{,}\DecValTok{14}\NormalTok{,}\DecValTok{15}\NormalTok{,}\DecValTok{16}\NormalTok{,}\DecValTok{17}\NormalTok{,}\DecValTok{18}\NormalTok{,}\DecValTok{31}\NormalTok{,}\DecValTok{32}\NormalTok{,}\DecValTok{33}\NormalTok{,}\DecValTok{34}\NormalTok{,}\DecValTok{35}\NormalTok{,}\DecValTok{36}\NormalTok{)])}
|
||
\end{Highlighting}
|
||
\end{Shaded}
|
||
|
||
\begin{verbatim}
|
||
## No id variables; using all as measure variables
|
||
\end{verbatim}
|
||
|
||
\begin{Shaded}
|
||
\begin{Highlighting}[]
|
||
\FunctionTok{ggplot}\NormalTok{(T\_long, }\FunctionTok{aes}\NormalTok{(}\AttributeTok{x =}\NormalTok{ value)) }\SpecialCharTok{+}
|
||
\FunctionTok{geom\_histogram}\NormalTok{(}\AttributeTok{binwidth =} \DecValTok{1}\NormalTok{, }\AttributeTok{fill =} \StringTok{"blue"}\NormalTok{, }\AttributeTok{color =} \StringTok{"black"}\NormalTok{, }\AttributeTok{alpha =} \FloatTok{0.7}\NormalTok{) }\SpecialCharTok{+}
|
||
\FunctionTok{facet\_wrap}\NormalTok{(}\SpecialCharTok{\textasciitilde{}}\NormalTok{variable,}\AttributeTok{scales =} \StringTok{"free"}\NormalTok{,}\AttributeTok{ncol=}\DecValTok{6}\NormalTok{) }\SpecialCharTok{+}
|
||
\FunctionTok{labs}\NormalTok{(}\AttributeTok{title =} \StringTok{"Histograms for Each Column"}\NormalTok{, }\AttributeTok{x =} \StringTok{"Values"}\NormalTok{, }\AttributeTok{y =} \StringTok{"Frequency"}\NormalTok{)}
|
||
\end{Highlighting}
|
||
\end{Shaded}
|
||
|
||
\includegraphics{Projet_files/figure-latex/unnamed-chunk-7-1.pdf}
|
||
|
||
Nous observons bien une concordance avec l'analyse des expressions des
|
||
gênes figure . EN effet, les histogrammes en rapport avec le traitement
|
||
1 sont très nettement regroupés vers 0, soit une expression relative des
|
||
gênes qui ne change peu. Les histogrammes pour les relevés des variables
|
||
en lien avec T2 et T3 sont tout aussi similaires aux résultats
|
||
précédents : La variance de l'expression relative des gênes est plus
|
||
élevée et on observe bien une polarisation
|
||
``sous-exprimé-''sur-exprimé'' sur les relevés à 6h. Attention, ici on
|
||
observe aussi que T2 et T3 n'ont pas leur effet caractéristique
|
||
directement : à 2h, la distribution de l'expression des genes semble
|
||
presque Gaussienne, et à 1h elle ne se distingue pas beaucoup du
|
||
traitement 1 avec un regroupement sur 0.
|
||
|
||
\subsubsection{boxplots pour faire joli}\label{boxplots-pour-faire-joli}
|
||
|
||
\begin{Shaded}
|
||
\begin{Highlighting}[]
|
||
\FunctionTok{ggplot}\NormalTok{(}\FunctionTok{melt}\NormalTok{(T[}\DecValTok{1}\SpecialCharTok{:}\DecValTok{18}\NormalTok{]),}\FunctionTok{aes}\NormalTok{(}\AttributeTok{x=}\NormalTok{variable,}\AttributeTok{y=}\NormalTok{value))}\SpecialCharTok{+}
|
||
\FunctionTok{geom\_boxplot}\NormalTok{()}\SpecialCharTok{+} \FunctionTok{theme}\NormalTok{(}\AttributeTok{axis.text.x =} \FunctionTok{element\_text}\NormalTok{(}\AttributeTok{angle=}\DecValTok{90}\NormalTok{, }\AttributeTok{vjust =} \FloatTok{0.5}\NormalTok{, }\AttributeTok{hjust =} \DecValTok{1}\NormalTok{))}
|
||
\end{Highlighting}
|
||
\end{Shaded}
|
||
|
||
\begin{verbatim}
|
||
## No id variables; using all as measure variables
|
||
\end{verbatim}
|
||
|
||
\includegraphics{Projet_files/figure-latex/unnamed-chunk-8-1.pdf}
|
||
|
||
\begin{Shaded}
|
||
\begin{Highlighting}[]
|
||
\FunctionTok{ggplot}\NormalTok{(}\FunctionTok{melt}\NormalTok{(T[}\DecValTok{19}\SpecialCharTok{:}\DecValTok{36}\NormalTok{]),}\FunctionTok{aes}\NormalTok{(}\AttributeTok{x=}\NormalTok{variable,}\AttributeTok{y=}\NormalTok{value))}\SpecialCharTok{+}
|
||
\FunctionTok{geom\_boxplot}\NormalTok{() }\SpecialCharTok{+} \FunctionTok{theme}\NormalTok{(}\AttributeTok{axis.text.x =} \FunctionTok{element\_text}\NormalTok{(}\AttributeTok{angle=}\DecValTok{90}\NormalTok{, }\AttributeTok{vjust =} \FloatTok{0.5}\NormalTok{, }\AttributeTok{hjust =} \DecValTok{1}\NormalTok{))}
|
||
\end{Highlighting}
|
||
\end{Shaded}
|
||
|
||
\begin{verbatim}
|
||
## No id variables; using all as measure variables
|
||
\end{verbatim}
|
||
|
||
\includegraphics{Projet_files/figure-latex/unnamed-chunk-8-2.pdf}
|
||
|
||
On voit que même sans réduire les données, chaque variable s'exprime
|
||
environ avec la même intensité.
|
||
|
||
\section{TODO : RAJOUTER LES BOXPLOTS PAIRE QUANTITATIF QUALITATIF POUR
|
||
DECELER UNE CORRELATION,
|
||
INUTILE}\label{todo-rajouter-les-boxplots-paire-quantitatif-qualitatif-pour-deceler-une-correlation-inutile}
|
||
|
||
\begin{Shaded}
|
||
\begin{Highlighting}[]
|
||
\CommentTok{\# traitement 1 corrélation avec l\textquotesingle{}expression des genes du T1 T2 et T3}
|
||
\FunctionTok{ggplot}\NormalTok{(T,}\FunctionTok{aes}\NormalTok{(}\AttributeTok{y=}\NormalTok{T}\SpecialCharTok{$}\NormalTok{T1\_6H\_R1,}\AttributeTok{x=}\NormalTok{T}\SpecialCharTok{$}\NormalTok{ExpT1))}\SpecialCharTok{+}
|
||
\FunctionTok{geom\_boxplot}\NormalTok{()}
|
||
\end{Highlighting}
|
||
\end{Shaded}
|
||
|
||
\begin{verbatim}
|
||
## Warning: Use of `T$ExpT1` is discouraged.
|
||
## i Use `ExpT1` instead.
|
||
\end{verbatim}
|
||
|
||
\begin{verbatim}
|
||
## Warning: Use of `T$T1_6H_R1` is discouraged.
|
||
## i Use `T1_6H_R1` instead.
|
||
\end{verbatim}
|
||
|
||
\includegraphics{Projet_files/figure-latex/unnamed-chunk-9-1.pdf}
|
||
|
||
\begin{Shaded}
|
||
\begin{Highlighting}[]
|
||
\FunctionTok{ggplot}\NormalTok{(T,}\FunctionTok{aes}\NormalTok{(}\AttributeTok{y=}\NormalTok{T}\SpecialCharTok{$}\NormalTok{T1\_6H\_R2,}\AttributeTok{x=}\NormalTok{T}\SpecialCharTok{$}\NormalTok{ExpT1))}\SpecialCharTok{+}
|
||
\FunctionTok{geom\_boxplot}\NormalTok{()}
|
||
\end{Highlighting}
|
||
\end{Shaded}
|
||
|
||
\begin{verbatim}
|
||
## Warning: Use of `T$ExpT1` is discouraged.
|
||
## i Use `ExpT1` instead.
|
||
\end{verbatim}
|
||
|
||
\begin{verbatim}
|
||
## Warning: Use of `T$T1_6H_R2` is discouraged.
|
||
## i Use `T1_6H_R2` instead.
|
||
\end{verbatim}
|
||
|
||
\includegraphics{Projet_files/figure-latex/unnamed-chunk-9-2.pdf}
|
||
|
||
\begin{Shaded}
|
||
\begin{Highlighting}[]
|
||
\FunctionTok{ggplot}\NormalTok{(T,}\FunctionTok{aes}\NormalTok{(}\AttributeTok{y=}\NormalTok{T}\SpecialCharTok{$}\NormalTok{T1\_6H\_R1,}\AttributeTok{x=}\NormalTok{T}\SpecialCharTok{$}\NormalTok{ExpT2))}\SpecialCharTok{+}
|
||
\FunctionTok{geom\_boxplot}\NormalTok{()}
|
||
\end{Highlighting}
|
||
\end{Shaded}
|
||
|
||
\begin{verbatim}
|
||
## Warning: Use of `T$ExpT2` is discouraged.
|
||
## i Use `ExpT2` instead.
|
||
\end{verbatim}
|
||
|
||
\begin{verbatim}
|
||
## Warning: Use of `T$T1_6H_R1` is discouraged.
|
||
## i Use `T1_6H_R1` instead.
|
||
\end{verbatim}
|
||
|
||
\includegraphics{Projet_files/figure-latex/unnamed-chunk-9-3.pdf}
|
||
|
||
\begin{Shaded}
|
||
\begin{Highlighting}[]
|
||
\FunctionTok{ggplot}\NormalTok{(T,}\FunctionTok{aes}\NormalTok{(}\AttributeTok{y=}\NormalTok{T}\SpecialCharTok{$}\NormalTok{T1\_6H\_R2,}\AttributeTok{x=}\NormalTok{T}\SpecialCharTok{$}\NormalTok{ExpT2))}\SpecialCharTok{+}
|
||
\FunctionTok{geom\_boxplot}\NormalTok{()}
|
||
\end{Highlighting}
|
||
\end{Shaded}
|
||
|
||
\begin{verbatim}
|
||
## Warning: Use of `T$ExpT2` is discouraged.
|
||
## i Use `ExpT2` instead.
|
||
\end{verbatim}
|
||
|
||
\begin{verbatim}
|
||
## Warning: Use of `T$T1_6H_R2` is discouraged.
|
||
## i Use `T1_6H_R2` instead.
|
||
\end{verbatim}
|
||
|
||
\includegraphics{Projet_files/figure-latex/unnamed-chunk-9-4.pdf}
|
||
|
||
\begin{Shaded}
|
||
\begin{Highlighting}[]
|
||
\FunctionTok{ggplot}\NormalTok{(T,}\FunctionTok{aes}\NormalTok{(}\AttributeTok{y=}\NormalTok{T}\SpecialCharTok{$}\NormalTok{T1\_6H\_R1,}\AttributeTok{x=}\NormalTok{T}\SpecialCharTok{$}\NormalTok{ExpT3))}\SpecialCharTok{+}
|
||
\FunctionTok{geom\_boxplot}\NormalTok{()}
|
||
\end{Highlighting}
|
||
\end{Shaded}
|
||
|
||
\begin{verbatim}
|
||
## Warning: Use of `T$ExpT3` is discouraged.
|
||
## i Use `ExpT3` instead.
|
||
\end{verbatim}
|
||
|
||
\begin{verbatim}
|
||
## Warning: Use of `T$T1_6H_R1` is discouraged.
|
||
## i Use `T1_6H_R1` instead.
|
||
\end{verbatim}
|
||
|
||
\includegraphics{Projet_files/figure-latex/unnamed-chunk-9-5.pdf}
|
||
|
||
\begin{Shaded}
|
||
\begin{Highlighting}[]
|
||
\FunctionTok{ggplot}\NormalTok{(T,}\FunctionTok{aes}\NormalTok{(}\AttributeTok{y=}\NormalTok{T}\SpecialCharTok{$}\NormalTok{T1\_6H\_R2,}\AttributeTok{x=}\NormalTok{T}\SpecialCharTok{$}\NormalTok{ExpT3))}\SpecialCharTok{+}
|
||
\FunctionTok{geom\_boxplot}\NormalTok{()}
|
||
\end{Highlighting}
|
||
\end{Shaded}
|
||
|
||
\begin{verbatim}
|
||
## Warning: Use of `T$ExpT3` is discouraged.
|
||
## i Use `ExpT3` instead.
|
||
\end{verbatim}
|
||
|
||
\begin{verbatim}
|
||
## Warning: Use of `T$T1_6H_R2` is discouraged.
|
||
## i Use `T1_6H_R2` instead.
|
||
\end{verbatim}
|
||
|
||
\includegraphics{Projet_files/figure-latex/unnamed-chunk-9-6.pdf}
|
||
|
||
\begin{Shaded}
|
||
\begin{Highlighting}[]
|
||
\CommentTok{\# traitement 2 corrélation avec l\textquotesingle{}expression des genes du T1 T2 et T3}
|
||
|
||
\FunctionTok{ggplot}\NormalTok{(T,}\FunctionTok{aes}\NormalTok{(}\AttributeTok{y=}\NormalTok{T}\SpecialCharTok{$}\NormalTok{T2\_6H\_R1,}\AttributeTok{x=}\NormalTok{T}\SpecialCharTok{$}\NormalTok{ExpT1))}\SpecialCharTok{+}
|
||
\FunctionTok{geom\_boxplot}\NormalTok{()}
|
||
\end{Highlighting}
|
||
\end{Shaded}
|
||
|
||
\begin{verbatim}
|
||
## Warning: Use of `T$ExpT1` is discouraged.
|
||
## i Use `ExpT1` instead.
|
||
\end{verbatim}
|
||
|
||
\begin{verbatim}
|
||
## Warning: Use of `T$T2_6H_R1` is discouraged.
|
||
## i Use `T2_6H_R1` instead.
|
||
\end{verbatim}
|
||
|
||
\includegraphics{Projet_files/figure-latex/unnamed-chunk-9-7.pdf}
|
||
|
||
\begin{Shaded}
|
||
\begin{Highlighting}[]
|
||
\FunctionTok{ggplot}\NormalTok{(T,}\FunctionTok{aes}\NormalTok{(}\AttributeTok{y=}\NormalTok{T}\SpecialCharTok{$}\NormalTok{T2\_6H\_R2,}\AttributeTok{x=}\NormalTok{T}\SpecialCharTok{$}\NormalTok{ExpT1))}\SpecialCharTok{+}
|
||
\FunctionTok{geom\_boxplot}\NormalTok{()}
|
||
\end{Highlighting}
|
||
\end{Shaded}
|
||
|
||
\begin{verbatim}
|
||
## Warning: Use of `T$ExpT1` is discouraged.
|
||
## i Use `ExpT1` instead.
|
||
\end{verbatim}
|
||
|
||
\begin{verbatim}
|
||
## Warning: Use of `T$T2_6H_R2` is discouraged.
|
||
## i Use `T2_6H_R2` instead.
|
||
\end{verbatim}
|
||
|
||
\includegraphics{Projet_files/figure-latex/unnamed-chunk-9-8.pdf}
|
||
|
||
\begin{Shaded}
|
||
\begin{Highlighting}[]
|
||
\FunctionTok{ggplot}\NormalTok{(T,}\FunctionTok{aes}\NormalTok{(}\AttributeTok{y=}\NormalTok{T}\SpecialCharTok{$}\NormalTok{T2\_6H\_R1,}\AttributeTok{x=}\NormalTok{T}\SpecialCharTok{$}\NormalTok{ExpT2))}\SpecialCharTok{+}
|
||
\FunctionTok{geom\_boxplot}\NormalTok{()}
|
||
\end{Highlighting}
|
||
\end{Shaded}
|
||
|
||
\begin{verbatim}
|
||
## Warning: Use of `T$ExpT2` is discouraged.
|
||
## i Use `ExpT2` instead.
|
||
\end{verbatim}
|
||
|
||
\begin{verbatim}
|
||
## Warning: Use of `T$T2_6H_R1` is discouraged.
|
||
## i Use `T2_6H_R1` instead.
|
||
\end{verbatim}
|
||
|
||
\includegraphics{Projet_files/figure-latex/unnamed-chunk-9-9.pdf}
|
||
|
||
\begin{Shaded}
|
||
\begin{Highlighting}[]
|
||
\FunctionTok{ggplot}\NormalTok{(T,}\FunctionTok{aes}\NormalTok{(}\AttributeTok{y=}\NormalTok{T}\SpecialCharTok{$}\NormalTok{T2\_6H\_R2,}\AttributeTok{x=}\NormalTok{T}\SpecialCharTok{$}\NormalTok{ExpT2))}\SpecialCharTok{+}
|
||
\FunctionTok{geom\_boxplot}\NormalTok{()}
|
||
\end{Highlighting}
|
||
\end{Shaded}
|
||
|
||
\begin{verbatim}
|
||
## Warning: Use of `T$ExpT2` is discouraged.
|
||
## i Use `ExpT2` instead.
|
||
\end{verbatim}
|
||
|
||
\begin{verbatim}
|
||
## Warning: Use of `T$T2_6H_R2` is discouraged.
|
||
## i Use `T2_6H_R2` instead.
|
||
\end{verbatim}
|
||
|
||
\includegraphics{Projet_files/figure-latex/unnamed-chunk-9-10.pdf}
|
||
|
||
\begin{Shaded}
|
||
\begin{Highlighting}[]
|
||
\FunctionTok{ggplot}\NormalTok{(T,}\FunctionTok{aes}\NormalTok{(}\AttributeTok{y=}\NormalTok{T}\SpecialCharTok{$}\NormalTok{T2\_6H\_R1,}\AttributeTok{x=}\NormalTok{T}\SpecialCharTok{$}\NormalTok{ExpT3))}\SpecialCharTok{+}
|
||
\FunctionTok{geom\_boxplot}\NormalTok{()}
|
||
\end{Highlighting}
|
||
\end{Shaded}
|
||
|
||
\begin{verbatim}
|
||
## Warning: Use of `T$ExpT3` is discouraged.
|
||
## i Use `ExpT3` instead.
|
||
\end{verbatim}
|
||
|
||
\begin{verbatim}
|
||
## Warning: Use of `T$T2_6H_R1` is discouraged.
|
||
## i Use `T2_6H_R1` instead.
|
||
\end{verbatim}
|
||
|
||
\includegraphics{Projet_files/figure-latex/unnamed-chunk-9-11.pdf}
|
||
|
||
\begin{Shaded}
|
||
\begin{Highlighting}[]
|
||
\FunctionTok{ggplot}\NormalTok{(T,}\FunctionTok{aes}\NormalTok{(}\AttributeTok{y=}\NormalTok{T}\SpecialCharTok{$}\NormalTok{T2\_6H\_R2,}\AttributeTok{x=}\NormalTok{T}\SpecialCharTok{$}\NormalTok{ExpT3))}\SpecialCharTok{+}
|
||
\FunctionTok{geom\_boxplot}\NormalTok{()}
|
||
\end{Highlighting}
|
||
\end{Shaded}
|
||
|
||
\begin{verbatim}
|
||
## Warning: Use of `T$ExpT3` is discouraged.
|
||
## i Use `ExpT3` instead.
|
||
\end{verbatim}
|
||
|
||
\begin{verbatim}
|
||
## Warning: Use of `T$T2_6H_R2` is discouraged.
|
||
## i Use `T2_6H_R2` instead.
|
||
\end{verbatim}
|
||
|
||
\includegraphics{Projet_files/figure-latex/unnamed-chunk-9-12.pdf}
|
||
|
||
\begin{Shaded}
|
||
\begin{Highlighting}[]
|
||
\CommentTok{\# traitement 2 corrélation avec l\textquotesingle{}expression des genes du T1 T2 et T3}
|
||
\FunctionTok{ggplot}\NormalTok{(T,}\FunctionTok{aes}\NormalTok{(}\AttributeTok{y=}\NormalTok{T}\SpecialCharTok{$}\NormalTok{T3\_6H\_R1,}\AttributeTok{x=}\NormalTok{T}\SpecialCharTok{$}\NormalTok{ExpT1))}\SpecialCharTok{+}
|
||
\FunctionTok{geom\_boxplot}\NormalTok{()}
|
||
\end{Highlighting}
|
||
\end{Shaded}
|
||
|
||
\begin{verbatim}
|
||
## Warning: Use of `T$ExpT1` is discouraged.
|
||
## i Use `ExpT1` instead.
|
||
\end{verbatim}
|
||
|
||
\begin{verbatim}
|
||
## Warning: Use of `T$T3_6H_R1` is discouraged.
|
||
## i Use `T3_6H_R1` instead.
|
||
\end{verbatim}
|
||
|
||
\includegraphics{Projet_files/figure-latex/unnamed-chunk-9-13.pdf}
|
||
|
||
\begin{Shaded}
|
||
\begin{Highlighting}[]
|
||
\FunctionTok{ggplot}\NormalTok{(T,}\FunctionTok{aes}\NormalTok{(}\AttributeTok{y=}\NormalTok{T}\SpecialCharTok{$}\NormalTok{T3\_6H\_R2,}\AttributeTok{x=}\NormalTok{T}\SpecialCharTok{$}\NormalTok{ExpT1))}\SpecialCharTok{+}
|
||
\FunctionTok{geom\_boxplot}\NormalTok{()}
|
||
\end{Highlighting}
|
||
\end{Shaded}
|
||
|
||
\begin{verbatim}
|
||
## Warning: Use of `T$ExpT1` is discouraged.
|
||
## i Use `ExpT1` instead.
|
||
\end{verbatim}
|
||
|
||
\begin{verbatim}
|
||
## Warning: Use of `T$T3_6H_R2` is discouraged.
|
||
## i Use `T3_6H_R2` instead.
|
||
\end{verbatim}
|
||
|
||
\includegraphics{Projet_files/figure-latex/unnamed-chunk-9-14.pdf}
|
||
|
||
\begin{Shaded}
|
||
\begin{Highlighting}[]
|
||
\FunctionTok{ggplot}\NormalTok{(T,}\FunctionTok{aes}\NormalTok{(}\AttributeTok{y=}\NormalTok{T}\SpecialCharTok{$}\NormalTok{T3\_6H\_R1,}\AttributeTok{x=}\NormalTok{T}\SpecialCharTok{$}\NormalTok{ExpT2))}\SpecialCharTok{+}
|
||
\FunctionTok{geom\_boxplot}\NormalTok{()}
|
||
\end{Highlighting}
|
||
\end{Shaded}
|
||
|
||
\begin{verbatim}
|
||
## Warning: Use of `T$ExpT2` is discouraged.
|
||
## i Use `ExpT2` instead.
|
||
\end{verbatim}
|
||
|
||
\begin{verbatim}
|
||
## Warning: Use of `T$T3_6H_R1` is discouraged.
|
||
## i Use `T3_6H_R1` instead.
|
||
\end{verbatim}
|
||
|
||
\includegraphics{Projet_files/figure-latex/unnamed-chunk-9-15.pdf}
|
||
|
||
\begin{Shaded}
|
||
\begin{Highlighting}[]
|
||
\FunctionTok{ggplot}\NormalTok{(T,}\FunctionTok{aes}\NormalTok{(}\AttributeTok{y=}\NormalTok{T}\SpecialCharTok{$}\NormalTok{T3\_6H\_R2,}\AttributeTok{x=}\NormalTok{T}\SpecialCharTok{$}\NormalTok{ExpT2))}\SpecialCharTok{+}
|
||
\FunctionTok{geom\_boxplot}\NormalTok{()}
|
||
\end{Highlighting}
|
||
\end{Shaded}
|
||
|
||
\begin{verbatim}
|
||
## Warning: Use of `T$ExpT2` is discouraged.
|
||
## i Use `ExpT2` instead.
|
||
\end{verbatim}
|
||
|
||
\begin{verbatim}
|
||
## Warning: Use of `T$T3_6H_R2` is discouraged.
|
||
## i Use `T3_6H_R2` instead.
|
||
\end{verbatim}
|
||
|
||
\includegraphics{Projet_files/figure-latex/unnamed-chunk-9-16.pdf}
|
||
|
||
\begin{Shaded}
|
||
\begin{Highlighting}[]
|
||
\FunctionTok{ggplot}\NormalTok{(T,}\FunctionTok{aes}\NormalTok{(}\AttributeTok{y=}\NormalTok{T}\SpecialCharTok{$}\NormalTok{T3\_6H\_R1,}\AttributeTok{x=}\NormalTok{T}\SpecialCharTok{$}\NormalTok{ExpT3))}\SpecialCharTok{+}
|
||
\FunctionTok{geom\_boxplot}\NormalTok{()}
|
||
\end{Highlighting}
|
||
\end{Shaded}
|
||
|
||
\begin{verbatim}
|
||
## Warning: Use of `T$ExpT3` is discouraged.
|
||
## i Use `ExpT3` instead.
|
||
\end{verbatim}
|
||
|
||
\begin{verbatim}
|
||
## Warning: Use of `T$T3_6H_R1` is discouraged.
|
||
## i Use `T3_6H_R1` instead.
|
||
\end{verbatim}
|
||
|
||
\includegraphics{Projet_files/figure-latex/unnamed-chunk-9-17.pdf}
|
||
|
||
\begin{Shaded}
|
||
\begin{Highlighting}[]
|
||
\FunctionTok{ggplot}\NormalTok{(T,}\FunctionTok{aes}\NormalTok{(}\AttributeTok{y=}\NormalTok{T}\SpecialCharTok{$}\NormalTok{T3\_6H\_R2,}\AttributeTok{x=}\NormalTok{T}\SpecialCharTok{$}\NormalTok{ExpT3))}\SpecialCharTok{+}
|
||
\FunctionTok{geom\_boxplot}\NormalTok{()}
|
||
\end{Highlighting}
|
||
\end{Shaded}
|
||
|
||
\begin{verbatim}
|
||
## Warning: Use of `T$ExpT3` is discouraged.
|
||
## i Use `ExpT3` instead.
|
||
\end{verbatim}
|
||
|
||
\begin{verbatim}
|
||
## Warning: Use of `T$T3_6H_R2` is discouraged.
|
||
## i Use `T3_6H_R2` instead.
|
||
\end{verbatim}
|
||
|
||
\includegraphics{Projet_files/figure-latex/unnamed-chunk-9-18.pdf}
|
||
Analyse des boxplots : - traitement 1 (réplicats 1 et 2) Les genes
|
||
sur-exprimés au T1 n'ont pas changé d'expression relativement à
|
||
l'absence de traitement durant le T2. Il est difficile d'observer une
|
||
catégorie de genes de T1 qui se soient sous exprimés dans T2. De même
|
||
pour la sur-expression dans T2.
|
||
|
||
Ceux qui s'étaient sur-exprimés au T1 ont affiché aucun changement
|
||
semblent ne pas avoir changé d'expression au T3 ( relativement à
|
||
l'absence de traitement).
|
||
|
||
Ceux qui n'avaient pas changés d'expression relative durant T1, se sont
|
||
sous exprimé ou sur exprimé. Il faut bien se rappeler que T1 ne cible
|
||
que très peu de genes donc ces observations sont cohérentes.
|
||
|
||
\begin{itemize}
|
||
\tightlist
|
||
\item
|
||
traitement 2 On observe une légère tendance des genes s'étant
|
||
sous-exprimé avec T1 à se sous exprimer avec T2 mais le reste des
|
||
boxplots ne permettent pas de relever quoi que ce soit par rapport à
|
||
T2.
|
||
\end{itemize}
|
||
|
||
En revanche, il est très clair que T2 et T3 ciblent les mêmes genes,
|
||
toutes les expressions relevées par T2 concordent aux modalités
|
||
qualitatives moyennes calculées sur T3.
|
||
|
||
\subsection{Analyse bi-dimensionnelle}\label{analyse-bi-dimensionnelle}
|
||
|
||
\subsubsection{matrice de correlation des variables
|
||
quantitatives}\label{matrice-de-correlation-des-variables-quantitatives}
|
||
|
||
\begin{Shaded}
|
||
\begin{Highlighting}[]
|
||
\NormalTok{cr }\OtherTok{=} \FunctionTok{cor}\NormalTok{(T[}\SpecialCharTok{{-}}\FunctionTok{c}\NormalTok{(}\DecValTok{37}\SpecialCharTok{:}\DecValTok{39}\NormalTok{)])}
|
||
\FunctionTok{corrplot}\NormalTok{(cr,}\AttributeTok{method=}\StringTok{"ellipse"}\NormalTok{, }\AttributeTok{type=}\StringTok{"lower"}\NormalTok{, }\AttributeTok{bg =} \StringTok{"lightgrey"}\NormalTok{)}
|
||
\end{Highlighting}
|
||
\end{Shaded}
|
||
|
||
\includegraphics{Projet_files/figure-latex/unnamed-chunk-10-1.pdf}
|
||
|
||
\subsubsection{Regression linéaire des variables 2 à 2
|
||
???}\label{regression-linuxe9aire-des-variables-2-uxe0-2}
|
||
|
||
\subsubsection{librairie biostatR}\label{librairie-biostatr}
|
||
|
||
\begin{Shaded}
|
||
\begin{Highlighting}[]
|
||
\FunctionTok{library}\NormalTok{(BioStatR)}
|
||
\CommentTok{\# Calculate eta² for Treatment 1}
|
||
\FunctionTok{print}\NormalTok{(}\StringTok{"T1 vs T2"}\NormalTok{)}
|
||
\end{Highlighting}
|
||
\end{Shaded}
|
||
|
||
\begin{verbatim}
|
||
## [1] "T1 vs T2"
|
||
\end{verbatim}
|
||
|
||
\begin{Shaded}
|
||
\begin{Highlighting}[]
|
||
\FunctionTok{eta2}\NormalTok{(T}\SpecialCharTok{$}\NormalTok{T1\_6H\_R1, T}\SpecialCharTok{$}\NormalTok{ExpT2)}
|
||
\end{Highlighting}
|
||
\end{Shaded}
|
||
|
||
\begin{verbatim}
|
||
## [1] 0.1874682
|
||
\end{verbatim}
|
||
|
||
\begin{Shaded}
|
||
\begin{Highlighting}[]
|
||
\FunctionTok{eta2}\NormalTok{(T}\SpecialCharTok{$}\NormalTok{T1\_6H\_R2, T}\SpecialCharTok{$}\NormalTok{ExpT2)}
|
||
\end{Highlighting}
|
||
\end{Shaded}
|
||
|
||
\begin{verbatim}
|
||
## [1] 0.1987298
|
||
\end{verbatim}
|
||
|
||
\begin{Shaded}
|
||
\begin{Highlighting}[]
|
||
\FunctionTok{print}\NormalTok{(}\StringTok{"T1 vs T3"}\NormalTok{)}
|
||
\end{Highlighting}
|
||
\end{Shaded}
|
||
|
||
\begin{verbatim}
|
||
## [1] "T1 vs T3"
|
||
\end{verbatim}
|
||
|
||
\begin{Shaded}
|
||
\begin{Highlighting}[]
|
||
\FunctionTok{eta2}\NormalTok{(T}\SpecialCharTok{$}\NormalTok{T1\_6H\_R1, T}\SpecialCharTok{$}\NormalTok{ExpT3)}
|
||
\end{Highlighting}
|
||
\end{Shaded}
|
||
|
||
\begin{verbatim}
|
||
## [1] 0.1516016
|
||
\end{verbatim}
|
||
|
||
\begin{Shaded}
|
||
\begin{Highlighting}[]
|
||
\FunctionTok{eta2}\NormalTok{(T}\SpecialCharTok{$}\NormalTok{T1\_6H\_R2, T}\SpecialCharTok{$}\NormalTok{ExpT3)}
|
||
\end{Highlighting}
|
||
\end{Shaded}
|
||
|
||
\begin{verbatim}
|
||
## [1] 0.1423772
|
||
\end{verbatim}
|
||
|
||
\begin{Shaded}
|
||
\begin{Highlighting}[]
|
||
\FunctionTok{print}\NormalTok{(}\StringTok{"T2 vs T3"}\NormalTok{)}
|
||
\end{Highlighting}
|
||
\end{Shaded}
|
||
|
||
\begin{verbatim}
|
||
## [1] "T2 vs T3"
|
||
\end{verbatim}
|
||
|
||
\begin{Shaded}
|
||
\begin{Highlighting}[]
|
||
\FunctionTok{eta2}\NormalTok{(T}\SpecialCharTok{$}\NormalTok{T2\_6H\_R1, T}\SpecialCharTok{$}\NormalTok{ExpT3)}
|
||
\end{Highlighting}
|
||
\end{Shaded}
|
||
|
||
\begin{verbatim}
|
||
## [1] 0.9022439
|
||
\end{verbatim}
|
||
|
||
\begin{Shaded}
|
||
\begin{Highlighting}[]
|
||
\FunctionTok{eta2}\NormalTok{(T}\SpecialCharTok{$}\NormalTok{T2\_6H\_R2, T}\SpecialCharTok{$}\NormalTok{ExpT3)}
|
||
\end{Highlighting}
|
||
\end{Shaded}
|
||
|
||
\begin{verbatim}
|
||
## [1] 0.8877959
|
||
\end{verbatim}
|
||
|
||
Le calcul du rapport de correlation eta² bien notre observation de la
|
||
grande similarité d'expression des genes traités avec T2 et T2 et la
|
||
dissimilarité des expression des genes lorsque la plante est traitée
|
||
avec T1 comparée à T2 et T3, chose normale au vu du peu de genes
|
||
affectés par T1.
|
||
|
||
\subsubsection{table de contingence pour les variables quali 2 à 2,
|
||
mosaic plot
|
||
?}\label{table-de-contingence-pour-les-variables-quali-2-uxe0-2-mosaic-plot}
|
||
|
||
\begin{Shaded}
|
||
\begin{Highlighting}[]
|
||
\FunctionTok{table}\NormalTok{(T}\SpecialCharTok{$}\NormalTok{ExpT1,T}\SpecialCharTok{$}\NormalTok{ExpT2)}
|
||
\end{Highlighting}
|
||
\end{Shaded}
|
||
|
||
\begin{verbatim}
|
||
##
|
||
## Non Sous Sur
|
||
## Non 0 178 263
|
||
## Sous 1 50 6
|
||
## Sur 10 19 15
|
||
\end{verbatim}
|
||
|
||
\begin{Shaded}
|
||
\begin{Highlighting}[]
|
||
\FunctionTok{table}\NormalTok{(T}\SpecialCharTok{$}\NormalTok{ExpT1,T}\SpecialCharTok{$}\NormalTok{ExpT3)}
|
||
\end{Highlighting}
|
||
\end{Shaded}
|
||
|
||
\begin{verbatim}
|
||
##
|
||
## Non Sous Sur
|
||
## Non 0 178 263
|
||
## Sous 0 51 6
|
||
## Sur 7 18 19
|
||
\end{verbatim}
|
||
|
||
\begin{Shaded}
|
||
\begin{Highlighting}[]
|
||
\FunctionTok{table}\NormalTok{(T}\SpecialCharTok{$}\NormalTok{ExpT2,T}\SpecialCharTok{$}\NormalTok{ExpT3)}
|
||
\end{Highlighting}
|
||
\end{Shaded}
|
||
|
||
\begin{verbatim}
|
||
##
|
||
## Non Sous Sur
|
||
## Non 6 1 4
|
||
## Sous 1 246 0
|
||
## Sur 0 0 284
|
||
\end{verbatim}
|
||
|
||
Nouvelle confirmation de nos résultats de manière encore plus précise,
|
||
on observe que T1 ne change pas l'expression de la très grande majorité
|
||
des genes. Plus finement, on peut confirmer l'observation faite sur les
|
||
boxplots tendant à dire que le peu de genes s'étant sous exprimés avec
|
||
T1 se sont aussi sous-exprimés avec T2 et T3.
|
||
|
||
La grande valeur des effectifs partiels sur la diagonale de la table de
|
||
contingence entre T2 et T3 montre bien la similarité de l'effet de ces
|
||
deux traitement sur l'expression des genes.
|
||
|
||
\subsection{Menez une analyse en composantes principales où les Tt sH Rr
|
||
sont les individus décrits par les
|
||
gènes.}\label{menez-une-analyse-en-composantes-principales-ouxf9-les-tt-sh-rr-sont-les-individus-duxe9crits-par-les-guxe8nes.}
|
||
|
||
Pour faire cela, nous devons transposer la matrice de données originale
|
||
qui elle décrivait les gènes (individus) en fonction des Tt sH Rr. Nous
|
||
décidons de faire directement une ACP sur un jeu de données centrées
|
||
réduites pour que chaque variable s'exprime avec la même force dans les
|
||
résultats et qu'ils soient lisibles.
|
||
|
||
\begin{Shaded}
|
||
\begin{Highlighting}[]
|
||
\NormalTok{donnees\_transposees }\OtherTok{=} \FunctionTok{t}\NormalTok{(T[}\SpecialCharTok{{-}}\FunctionTok{c}\NormalTok{(}\DecValTok{37}\SpecialCharTok{:}\DecValTok{39}\NormalTok{)])}
|
||
\NormalTok{res\_pca}\OtherTok{\textless{}{-}}\FunctionTok{PCA}\NormalTok{(donnees\_transposees,}\AttributeTok{scale.unit=}\ConstantTok{TRUE}\NormalTok{,}\AttributeTok{graph=}\ConstantTok{FALSE}\NormalTok{)}
|
||
\NormalTok{res\_pca}\SpecialCharTok{$}\NormalTok{eig}
|
||
\end{Highlighting}
|
||
\end{Shaded}
|
||
|
||
\begin{verbatim}
|
||
## eigenvalue percentage of variance cumulative percentage of variance
|
||
## comp 1 385.4885605 71.12335064 71.12335
|
||
## comp 2 56.8398561 10.48705833 81.61041
|
||
## comp 3 18.8058681 3.46971736 85.08013
|
||
## comp 4 17.3534861 3.20175019 88.28188
|
||
## comp 5 16.2400069 2.99631123 91.27819
|
||
## comp 6 9.3466113 1.72446702 93.00265
|
||
## comp 7 6.3208427 1.16620715 94.16886
|
||
## comp 8 4.6888314 0.86509805 95.03396
|
||
## comp 9 2.8880421 0.53284909 95.56681
|
||
## comp 10 2.6663658 0.49194941 96.05876
|
||
## comp 11 2.4741195 0.45647962 96.51524
|
||
## comp 12 1.8835315 0.34751504 96.86275
|
||
## comp 13 1.7438070 0.32173561 97.18449
|
||
## comp 14 1.6614064 0.30653255 97.49102
|
||
## comp 15 1.5634400 0.28845757 97.77948
|
||
## comp 16 1.2936620 0.23868302 98.01816
|
||
## comp 17 1.2002743 0.22145283 98.23961
|
||
## comp 18 1.0809897 0.19944460 98.43906
|
||
## comp 19 0.8153461 0.15043286 98.58949
|
||
## comp 20 0.7943348 0.14655624 98.73605
|
||
## comp 21 0.7596276 0.14015270 98.87620
|
||
## comp 22 0.6964670 0.12849944 99.00470
|
||
## comp 23 0.6303898 0.11630808 99.12101
|
||
## comp 24 0.6030871 0.11127068 99.23228
|
||
## comp 25 0.5412364 0.09985912 99.33214
|
||
## comp 26 0.4619356 0.08522796 99.41737
|
||
## comp 27 0.4395132 0.08109100 99.49846
|
||
## comp 28 0.4332061 0.07992733 99.57838
|
||
## comp 29 0.4110199 0.07583392 99.65422
|
||
## comp 30 0.3506662 0.06469855 99.71892
|
||
## comp 31 0.3429738 0.06327930 99.78220
|
||
## comp 32 0.3356932 0.06193601 99.84413
|
||
## comp 33 0.3238087 0.05974330 99.90388
|
||
## comp 34 0.2870588 0.05296288 99.95684
|
||
## comp 35 0.2339343 0.04316132 100.00000
|
||
\end{verbatim}
|
||
|
||
\begin{Shaded}
|
||
\begin{Highlighting}[]
|
||
\FunctionTok{fviz\_eig}\NormalTok{(res\_pca)}
|
||
\end{Highlighting}
|
||
\end{Shaded}
|
||
|
||
\includegraphics{Projet_files/figure-latex/unnamed-chunk-13-1.pdf} Ce
|
||
graphique représente les valeurs propres de la matrice de corrélation du
|
||
jeu de données centré réduites. L'inertie totale des données étant la
|
||
somme des valeurs propres ( qui elles sont les inerties axiale associées
|
||
à l'axe de vecteur directeur un vecteur propre associé ), chaque valeur
|
||
propre est donc une fraction de l'inertie totale. On voit qu'on dépasse
|
||
80\% de l'inertie totale des points rien qu'avec les deux premieres
|
||
valeurs propres, on en prend donc deux vectueurs propres associés
|
||
respectivement à chacune de ces deux valeurs propres comme axes
|
||
principaux de l'analyse.
|
||
|
||
\begin{Shaded}
|
||
\begin{Highlighting}[]
|
||
\FunctionTok{fviz\_pca\_ind}\NormalTok{(res\_pca,}\AttributeTok{label=}\StringTok{"all"}\NormalTok{)}
|
||
\end{Highlighting}
|
||
\end{Shaded}
|
||
|
||
\includegraphics{Projet_files/figure-latex/unnamed-chunk-14-1.pdf}
|
||
|
||
\begin{Shaded}
|
||
\begin{Highlighting}[]
|
||
\FunctionTok{fviz\_pca\_var}\NormalTok{(res\_pca,}\AttributeTok{axes=}\FunctionTok{c}\NormalTok{(}\DecValTok{1}\NormalTok{,}\DecValTok{2}\NormalTok{),}\AttributeTok{label=}\StringTok{"none"}\NormalTok{)}
|
||
\end{Highlighting}
|
||
\end{Shaded}
|
||
|
||
\includegraphics{Projet_files/figure-latex/unnamed-chunk-14-2.pdf}
|
||
Contexte : les relevés aux heures sont décrits par les gènes ( les gènes
|
||
sont considérés comme les variables).
|
||
|
||
\begin{itemize}
|
||
\tightlist
|
||
\item
|
||
les genes proches d'un axe sont très représentés par celui-ci
|
||
\item
|
||
les genes dont l'angle entre eux est petit sont corrélés entre eux
|
||
\end{itemize}
|
||
|
||
\subsection{Interprétation globale du couple de
|
||
graphes}\label{interpruxe9tation-globale-du-couple-de-graphes}
|
||
|
||
On voit que les genes se polarisent principalement sur l'axe 1 dans un
|
||
sens ou l'autre. Les flèches sont d'une longueur presque du rayon du
|
||
cercle, indiquant une participation très forte des genes dans la
|
||
variance expliquée par ces dimensions. Il n'y a pas de tendance
|
||
particulière sur la direction selon l'axe 2 des flèches : Dans chaque
|
||
``polarité'' de fleches selon l'axe 1, il y a des fleches dont la
|
||
direction est negative d'autres positive selon l'axe 2.
|
||
|
||
Le traitement 1 est entièrement groupé sur des valeurs très negatives de
|
||
l'axe 1. On remarque dans ce groupement la présence des T3 et T4 à la
|
||
première heure de relevés d'expression des gènes.
|
||
|
||
\subsection{ON EST SENSE VOIR UN TRUC IMPORTANT D'APRES LA PROF MAIS JE
|
||
VOIS
|
||
RIEN}\label{on-est-sense-voir-un-truc-important-dapres-la-prof-mais-je-vois-rien}
|
||
|
||
\subsubsection{Les axes générés par l'ACP sont purement virtuels, mais
|
||
on peut y préter un sens plus ou moins défini selon les variables qui y
|
||
sont
|
||
corrélées}\label{les-axes-guxe9nuxe9ruxe9s-par-lacp-sont-purement-virtuels-mais-on-peut-y-pruxe9ter-un-sens-plus-ou-moins-duxe9fini-selon-les-variables-qui-y-sont-corruxe9luxe9es}
|
||
|
||
axe 1: force du changement d'expression des gènes : si on
|
||
sur-exprime/sous-exprime de beaucoup ( genre 0=\textgreater5) ou pas,
|
||
polarisation ?
|
||
|
||
axe 2 : vers le haut =\textgreater{} ça va changer d'expression bientot,
|
||
vers le bas =\textgreater{} ça se stabilise ( donc les genes pointant
|
||
vers le haut changent d'expression, et ceux vers le bas ont tendance à
|
||
rester plutot pareil )
|
||
|
||
\paragraph{On remarque que les traitements ne sont pas du tout décris de
|
||
la même manière selon les horaires mais il y a une régularité
|
||
d'apparition dans chaque tranche
|
||
horaire.}\label{on-remarque-que-les-traitements-ne-sont-pas-du-tout-duxe9cris-de-la-muxeame-maniuxe8re-selon-les-horaires-mais-il-y-a-une-ruxe9gularituxe9-dapparition-dans-chaque-tranche-horaire.}
|
||
|
||
\subsubsection{hypothèses sur la signification : qu'est-ce qu'ils ont en
|
||
commun ces gènes qui pourrait décrire ces relevés aux différentes heures
|
||
et les différents
|
||
traitements}\label{hypothuxe8ses-sur-la-signification-quest-ce-quils-ont-en-commun-ces-guxe8nes-qui-pourrait-duxe9crire-ces-relevuxe9s-aux-diffuxe9rentes-heures-et-les-diffuxe9rents-traitements}
|
||
|
||
En regardant le graphe des individus (résultats aux heures de relevés),
|
||
on a effectivement les heures groupées à des valeurs negatives de l'axe
|
||
1 correspondant aux relevés du traitement 1 qui, souvenons-nous toujours
|
||
des histogrammes, ne change l'expression relative que de très peu de
|
||
gènes.
|
||
|
||
Pour l'interprétation du second axe, les gènes semblent y être
|
||
positivement et negativement corrélés quel que soit leur correlation
|
||
avec l'axe 1. En regardant les individus, on observe que plus l'heure
|
||
est tardive, plus ils tendent vers des valeurs negatives sur l'axe 2. De
|
||
plus, on observe que les points liés aux relevés du traitement 1 ne vont
|
||
pas énormément vers les valeurs positives. Il semble donc que l'axe 2
|
||
soit indicateur des expressions des gènes sont susceptibles de changer.
|
||
|
||
\subsubsection{afin de visualiser les corrélations des variables
|
||
intiales avec toutes les méta-variables (pas trs utile on a déjà le
|
||
cercle)}\label{afin-de-visualiser-les-corruxe9lations-des-variables-intiales-avec-toutes-les-muxe9ta-variables-pas-trs-utile-on-a-duxe9juxe0-le-cercle}
|
||
|
||
\begin{Shaded}
|
||
\begin{Highlighting}[]
|
||
\CommentTok{\# que 50 gènes sinon c\textquotesingle{}est le bordel}
|
||
\FunctionTok{corrplot}\NormalTok{(res\_pca}\SpecialCharTok{$}\NormalTok{var}\SpecialCharTok{$}\NormalTok{cor[}\DecValTok{1}\SpecialCharTok{:}\DecValTok{50}\NormalTok{,],}\AttributeTok{method=}\StringTok{"ellipse"}\NormalTok{, }\AttributeTok{type=}\StringTok{"lower"}\NormalTok{, }\AttributeTok{bg =} \StringTok{"lightgrey"}\NormalTok{)}
|
||
\end{Highlighting}
|
||
\end{Shaded}
|
||
|
||
\includegraphics{Projet_files/figure-latex/unnamed-chunk-15-1.pdf}
|
||
|
||
MAIS C'EST INBUVABLE
|
||
|
||
\begin{Shaded}
|
||
\begin{Highlighting}[]
|
||
\FunctionTok{fviz\_pca\_ind}\NormalTok{(res\_pca,}\AttributeTok{axes =} \FunctionTok{c}\NormalTok{(}\DecValTok{1}\NormalTok{,}\DecValTok{3}\NormalTok{),}\AttributeTok{geom=}\FunctionTok{c}\NormalTok{(}\StringTok{"point"}\NormalTok{))}
|
||
\end{Highlighting}
|
||
\end{Shaded}
|
||
|
||
\includegraphics{Projet_files/figure-latex/unnamed-chunk-16-1.pdf}
|
||
|
||
\begin{Shaded}
|
||
\begin{Highlighting}[]
|
||
\FunctionTok{fviz\_pca\_ind}\NormalTok{(res\_pca,}\AttributeTok{axes =} \FunctionTok{c}\NormalTok{(}\DecValTok{1}\NormalTok{,}\DecValTok{4}\NormalTok{),}\AttributeTok{geom=}\FunctionTok{c}\NormalTok{(}\StringTok{"point"}\NormalTok{))}
|
||
\end{Highlighting}
|
||
\end{Shaded}
|
||
|
||
\includegraphics{Projet_files/figure-latex/unnamed-chunk-16-2.pdf}
|
||
|
||
\begin{Shaded}
|
||
\begin{Highlighting}[]
|
||
\FunctionTok{fviz\_pca\_ind}\NormalTok{(res\_pca,}\AttributeTok{axes =} \FunctionTok{c}\NormalTok{(}\DecValTok{1}\NormalTok{,}\DecValTok{5}\NormalTok{),}\AttributeTok{geom=}\FunctionTok{c}\NormalTok{(}\StringTok{"point"}\NormalTok{))}
|
||
\end{Highlighting}
|
||
\end{Shaded}
|
||
|
||
\includegraphics{Projet_files/figure-latex/unnamed-chunk-16-3.pdf}
|
||
|
||
\end{document}
|