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M1 BBS Graphes TP Recherche de communautés dans les graphes2.0 - Revision history
2024-03-28T20:22:09Z
Revision history for this page on the wiki
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Quentin: /* Propriétés des composantes connexes */
2022-11-29T14:17:47Z
<p><span class="autocomment">Propriétés des composantes connexes</span></p>
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<td colspan='2' style="background-color: white; color:black;">← Older revision</td>
<td colspan='2' style="background-color: white; color:black;">Revision as of 14:17, 29 November 2022</td>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>*Ajoutez la courbe correspondant au nombre d'arêtes maximum d'un graphe en fonction du nombre de sommets (fonction ''curve()'').</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>*Ajoutez la courbe correspondant au nombre d'arêtes maximum d'un graphe en fonction du nombre de sommets (fonction ''curve()'').</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div><del style="color: red; font-weight: bold; text-decoration: none;">++</del></div></td><td colspan="2"> </td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><source lang='rsplus'></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><source lang='rsplus'></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>xlimit <- 22</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>xlimit <- 22</div></td></tr>
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Quentin: /* Inspection des liens d'orthologies */
2022-11-29T13:40:59Z
<p><span class="autocomment">Inspection des liens d'orthologies</span></p>
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<td colspan='2' style="background-color: white; color:black;">← Older revision</td>
<td colspan='2' style="background-color: white; color:black;">Revision as of 13:40, 29 November 2022</td>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>++</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>++</div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div><del style="color: red; font-weight: bold; text-decoration: none;"><!--</del></div></td><td colspan="2"> </td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><source lang='rsplus'></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><source lang='rsplus'></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>YpesA <- genome_table %>% </div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>YpesA <- genome_table %>% </div></td></tr>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>cat("Sur les ", YpesA$Proteome, " proteines de YpesA, seules ", YpesA.Protein.Hits, " ont au moins un alignement avec YpesB.", sep="")</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>cat("Sur les ", YpesA$Proteome, " proteines de YpesA, seules ", YpesA.Protein.Hits, " ont au moins un alignement avec YpesB.", sep="")</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div></source></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div></source></div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div><del style="color: red; font-weight: bold; text-decoration: none;">--></del></div></td><td colspan="2"> </td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><!--</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><!--</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>old</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>old</div></td></tr>
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Quentin: /* Inspection des liens d'orthologies */
2022-11-29T13:31:34Z
<p><span class="autocomment">Inspection des liens d'orthologies</span></p>
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<td colspan='2' style="background-color: white; color:black;">← Older revision</td>
<td colspan='2' style="background-color: white; color:black;">Revision as of 13:31, 29 November 2022</td>
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<tr><td colspan="2" class="diff-lineno">Line 218:</td>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>++</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>++</div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div><del style="color: red; font-weight: bold; text-decoration: none;"><!--</del></div></td><td colspan="2"> </td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><source lang='rsplus'></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><source lang='rsplus'></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>max_hits <- nbaliprot %>% </div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>max_hits <- nbaliprot %>% </div></td></tr>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>kable(compact)</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>kable(compact)</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div></source></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div></source></div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div><del class="diffchange diffchange-inline">--></del></div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div> </div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>*Est-ce que toutes les protéines de A ont un alignement dans B?</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>*Est-ce que toutes les protéines de A ont un alignement dans B?</div></td></tr>
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Quentin: /* Inspection des liens d'orthologies */
2022-11-29T13:24:39Z
<p><span class="autocomment">Inspection des liens d'orthologies</span></p>
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<td colspan='2' style="background-color: white; color:black;">← Older revision</td>
<td colspan='2' style="background-color: white; color:black;">Revision as of 13:24, 29 November 2022</td>
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<tr><td colspan="2" class="diff-lineno">Line 180:</td>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>++</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>++</div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div><del style="color: red; font-weight: bold; text-decoration: none;"><!--</del></div></td><td colspan="2"> </td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><source lang='rsplus'></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><source lang='rsplus'></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>nbaliprot <- homologs %>% </div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>nbaliprot <- homologs %>% </div></td></tr>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div> arrange(desc(Hits))</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div> arrange(desc(Hits))</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div></source></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div></source></div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div><del style="color: red; font-weight: bold; text-decoration: none;">--></del></div></td><td colspan="2"> </td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>*Tracez la distribution du nombre d'alignement par protéine avec ''geom_histogram(binwidth=1, col=color, fill=color)''.</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>*Tracez la distribution du nombre d'alignement par protéine avec ''geom_histogram(binwidth=1, col=color, fill=color)''.</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>++</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>++</div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div><del style="color: red; font-weight: bold; text-decoration: none;"><!--</del></div></td><td colspan="2"> </td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><source lang='rsplus'></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><source lang='rsplus'></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>ggplot(nbaliprot, aes(x=Hits)) + </div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>ggplot(nbaliprot, aes(x=Hits)) + </div></td></tr>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div> theme_bw()</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div> theme_bw()</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div></source></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div></source></div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div><del style="color: red; font-weight: bold; text-decoration: none;">--></del></div></td><td colspan="2"> </td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><!--</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><!--</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>ancienne version</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>ancienne version</div></td></tr>
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Quentin: /* Tableau de données */
2022-11-29T13:18:00Z
<p><span class="autocomment">Tableau de données</span></p>
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<td colspan='2' style="background-color: white; color:black;">Revision as of 13:18, 29 November 2022</td>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>++</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>++</div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div><del style="color: red; font-weight: bold; text-decoration: none;"><!--</del></div></td><td colspan="2"> </td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><source lang='rsplus'></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><source lang='rsplus'></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>boxplot(genome_table$Proteome, ylab='Proteome size', col='coral', las=1)</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>boxplot(genome_table$Proteome, ylab='Proteome size', col='coral', las=1)</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div></source></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div></source></div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div><del style="color: red; font-weight: bold; text-decoration: none;">--></del></div></td><td colspan="2"> </td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><!--</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><!--</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><source lang='rsplus'></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><source lang='rsplus'></div></td></tr>
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Quentin: /* Tableau de données */
2022-11-29T13:11:51Z
<p><span class="autocomment">Tableau de données</span></p>
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<td colspan='2' style="background-color: white; color:black;">Revision as of 13:11, 29 November 2022</td>
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<tr><td colspan="2" class="diff-lineno">Line 130:</td>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>++</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>++</div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div><del class="diffchange diffchange-inline"><!--</del></div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div> </div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><source lang='rsplus'></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><source lang='rsplus'></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>in_files <- c()</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>in_files <- c()</div></td></tr>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>kable(genome_table)</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>kable(genome_table)</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div></source></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div></source></div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div><del style="color: red; font-weight: bold; text-decoration: none;">--></del></div></td><td colspan="2"> </td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>*Tracer la distribution de la taille des protéomes (avec '''boxplot()''').</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>*Tracer la distribution de la taille des protéomes (avec '''boxplot()''').</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td></tr>
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Quentin: /* Inspection des liens d'orthologies */
2022-11-28T14:03:44Z
<p><span class="autocomment">Inspection des liens d'orthologies</span></p>
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<td colspan='2' style="background-color: white; color:black;">← Older revision</td>
<td colspan='2' style="background-color: white; color:black;">Revision as of 14:03, 28 November 2022</td>
</tr>
<tr><td colspan="2" class="diff-lineno">Line 183:</td>
<td colspan="2" class="diff-lineno">Line 183:</td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>++</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>++</div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;"><!--</ins></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><source lang='rsplus'></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><source lang='rsplus'></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>nbaliprot <- homologs %>% </div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>nbaliprot <- homologs %>% </div></td></tr>
<tr><td colspan="2" class="diff-lineno">Line 189:</td>
<td colspan="2" class="diff-lineno">Line 190:</td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div> arrange(desc(Hits))</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div> arrange(desc(Hits))</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div></source></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div></source></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;">--></ins></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>*Tracez la distribution du nombre d'alignement par protéine avec ''geom_histogram(binwidth=1, col=color, fill=color)''.</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>*Tracez la distribution du nombre d'alignement par protéine avec ''geom_histogram(binwidth=1, col=color, fill=color)''.</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td></tr>
<tr><td colspan="2" class="diff-lineno">Line 207:</td>
<td colspan="2" class="diff-lineno">Line 209:</td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div></source></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div></source></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>--></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>--></div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>*Identifiez la protéine qui a le plus d'alignements et analysez les alignements obtenus.</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>* Identifiez la protéine qui a le plus d'alignements et analysez les alignements obtenus.</div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div><del class="diffchange diffchange-inline">++</del></div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div> </div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><!-- </div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><!-- </div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>old version</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>old version</div></td></tr>
<tr><td colspan="2" class="diff-lineno">Line 223:</td>
<td colspan="2" class="diff-lineno">Line 225:</td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>++</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>++</div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;"><!--</ins></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><source lang='rsplus'></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><source lang='rsplus'></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>max_hits <- nbaliprot %>% </div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>max_hits <- nbaliprot %>% </div></td></tr>
<tr><td colspan="2" class="diff-lineno">Line 239:</td>
<td colspan="2" class="diff-lineno">Line 242:</td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>kable(compact)</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>kable(compact)</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div></source></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div></source></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;">--></ins></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>*Est-ce que toutes les protéines de A ont un alignement dans B?</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>*Est-ce que toutes les protéines de A ont un alignement dans B?</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td></tr>
<!-- diff generator: internal 2024-03-28 20:22:09 -->
</table>
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Quentin: /* Inspection des liens d'orthologies */
2022-11-28T14:02:11Z
<p><span class="autocomment">Inspection des liens d'orthologies</span></p>
<table style="background-color: white; color:black;">
<col class='diff-marker' />
<col class='diff-content' />
<col class='diff-marker' />
<col class='diff-content' />
<tr valign='top'>
<td colspan='2' style="background-color: white; color:black;">← Older revision</td>
<td colspan='2' style="background-color: white; color:black;">Revision as of 14:02, 28 November 2022</td>
</tr>
<tr><td colspan="2" class="diff-lineno">Line 181:</td>
<td colspan="2" class="diff-lineno">Line 181:</td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>*Combien d'alignement(s) attendez-vous par protéines?</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>*Combien d'alignement(s) attendez-vous par protéines?</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>Vous pouvez regrouper les lignes par requête (''group_by''(Query)) et compter le nombre de cibles (''summarise''(Hits=n())) pour chaque requête. </div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>Vous pouvez regrouper les lignes par requête (''group_by''(Query)) et compter le nombre de cibles (''summarise''(Hits=n())) pour chaque requête. </div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;"></ins></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>++</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>++</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><source lang='rsplus'></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><source lang='rsplus'></div></td></tr>
<tr><td colspan="2" class="diff-lineno">Line 189:</td>
<td colspan="2" class="diff-lineno">Line 190:</td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div></source></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div></source></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>*Tracez la distribution du nombre d'alignement par protéine avec ''geom_histogram(binwidth=1, col=color, fill=color)''.</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>*Tracez la distribution du nombre d'alignement par protéine avec ''geom_histogram(binwidth=1, col=color, fill=color)''.</div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;"></ins></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>++</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>++</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><!--</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><!--</div></td></tr>
<tr><td colspan="2" class="diff-lineno">Line 219:</td>
<td colspan="2" class="diff-lineno">Line 221:</td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>* sélectionner les colonnes: Query, Hit, Query.start, Query.end, Hit.start et Hit.end</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>* sélectionner les colonnes: Query, Hit, Query.start, Query.end, Hit.start et Hit.end</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>* éditer cette table avec kable.</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>* éditer cette table avec kable.</div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;"></ins></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>++</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>++</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><source lang='rsplus'></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><source lang='rsplus'></div></td></tr>
<tr><td colspan="2" class="diff-lineno">Line 237:</td>
<td colspan="2" class="diff-lineno">Line 240:</td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div></source></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div></source></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>*Est-ce que toutes les protéines de A ont un alignement dans B?</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>*Est-ce que toutes les protéines de A ont un alignement dans B?</div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;"></ins></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>++</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>++</div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;"><!--</ins></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><source lang='rsplus'></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><source lang='rsplus'></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>YpesA <- genome_table %>% </div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>YpesA <- genome_table %>% </div></td></tr>
<tr><td colspan="2" class="diff-lineno">Line 246:</td>
<td colspan="2" class="diff-lineno">Line 251:</td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>cat("Sur les ", YpesA$Proteome, " proteines de YpesA, seules ", YpesA.Protein.Hits, " ont au moins un alignement avec YpesB.", sep="")</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>cat("Sur les ", YpesA$Proteome, " proteines de YpesA, seules ", YpesA.Protein.Hits, " ont au moins un alignement avec YpesB.", sep="")</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div></source></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div></source></div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div> </div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins class="diffchange diffchange-inline">--></ins></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><!--</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><!--</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>old</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>old</div></td></tr>
<!-- diff generator: internal 2024-03-28 20:22:09 -->
</table>
Quentin
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Quentin: /* Inspection des liens d'orthologies */
2022-11-28T14:00:37Z
<p><span class="autocomment">Inspection des liens d'orthologies</span></p>
<table style="background-color: white; color:black;">
<col class='diff-marker' />
<col class='diff-content' />
<col class='diff-marker' />
<col class='diff-content' />
<tr valign='top'>
<td colspan='2' style="background-color: white; color:black;">← Older revision</td>
<td colspan='2' style="background-color: white; color:black;">Revision as of 14:00, 28 November 2022</td>
</tr>
<tr><td colspan="2" class="diff-lineno">Line 190:</td>
<td colspan="2" class="diff-lineno">Line 190:</td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>*Tracez la distribution du nombre d'alignement par protéine avec ''geom_histogram(binwidth=1, col=color, fill=color)''.</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>*Tracez la distribution du nombre d'alignement par protéine avec ''geom_histogram(binwidth=1, col=color, fill=color)''.</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>++</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>++</div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;"><!--</ins></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><source lang='rsplus'></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><source lang='rsplus'></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>ggplot(nbaliprot, aes(x=Hits)) + </div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>ggplot(nbaliprot, aes(x=Hits)) + </div></td></tr>
<tr><td colspan="2" class="diff-lineno">Line 196:</td>
<td colspan="2" class="diff-lineno">Line 197:</td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div> theme_bw()</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div> theme_bw()</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div></source></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div></source></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;">--></ins></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><!--</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><!--</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>ancienne version</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>ancienne version</div></td></tr>
<!-- diff generator: internal 2024-03-28 20:22:09 -->
</table>
Quentin
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Quentin: /* Tableau de données */
2022-11-28T13:59:52Z
<p><span class="autocomment">Tableau de données</span></p>
<table style="background-color: white; color:black;">
<col class='diff-marker' />
<col class='diff-content' />
<col class='diff-marker' />
<col class='diff-content' />
<tr valign='top'>
<td colspan='2' style="background-color: white; color:black;">← Older revision</td>
<td colspan='2' style="background-color: white; color:black;">Revision as of 13:59, 28 November 2022</td>
</tr>
<tr><td colspan="2" class="diff-lineno">Line 130:</td>
<td colspan="2" class="diff-lineno">Line 130:</td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>++</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>++</div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;"><!--</ins></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><source lang='rsplus'></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><source lang='rsplus'></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>in_files <- c()</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>in_files <- c()</div></td></tr>
<tr><td colspan="2" class="diff-lineno">Line 142:</td>
<td colspan="2" class="diff-lineno">Line 143:</td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>kable(genome_table)</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>kable(genome_table)</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div></source></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div></source></div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div> </div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins class="diffchange diffchange-inline">--></ins></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>*Tracer la distribution de la taille des protéomes (avec '''boxplot()''').</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>*Tracer la distribution de la taille des protéomes (avec '''boxplot()''').</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>++</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>++</div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;"><!--</ins></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><source lang='rsplus'></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><source lang='rsplus'></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>boxplot(genome_table$Proteome, ylab='Proteome size', col='coral', las=1)</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>boxplot(genome_table$Proteome, ylab='Proteome size', col='coral', las=1)</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div></source></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div></source></div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div> </div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins class="diffchange diffchange-inline">--></ins></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><!--</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><!--</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><source lang='rsplus'></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><source lang='rsplus'></div></td></tr>
<!-- diff generator: internal 2024-03-28 20:22:09 -->
</table>
Quentin