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Commit 8ebefab1 authored by Saskia Hiltemann's avatar Saskia Hiltemann
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        <dd><pre class="code file rsplus"><span class="co1"># 3d R plot</span>
        saveat <span class="sy0">&lt;-</span> <span class="st0">&quot;/mnt/NAS_coruscant_datashare/haasf/madland_RNA-seq_Hoecker&quot;</span>
        &nbsp;
        file.<span class="me1">rpkm</span> <span class="sy0">&lt;-</span> <span class="st0">'/mnt/NAS_coruscant_datashare/haasf/madland_RNA-seq_Hoecker/31315.p.sort.rpkm'</span>
        &nbsp;
        &nbsp;
        <span class="co1">## Windows ###</span>
        <span class="co1">#-#saveat &lt;- &quot;Q:/haasf/leubner_RNA-seq/Celery/DEGs_0.9/&quot;</span>
        &nbsp;
        <span class="co1">#-#file.rpkm &lt;- 'Q:/haasf/leubner_RNA-seq/Celery/DEGs/Celery_merged_isoforms.p.sort.rpkm'</span>
        <span class="co1">#-#file.count &lt;- 'Q:/haasf/leubner_RNA-seq/Celery/DEGs_0.9/Celery_merged_isoforms.p.sort.counts'</span>
        <span class="co1">###</span>
        &nbsp;
        data.<span class="me1">rpkm</span> <span class="sy0">&lt;-</span> <a href="http://stat.ethz.ch/R-manual/R-devel/library/utils/html/read.table.html"><span class="kw8">read.<span class="me1">table</span></span></a><span class="br0">&#40;</span>file.<span class="me1">rpkm</span>, header<span class="sy0">=</span><a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/T.html"><span class="kw2">T</span></a>, sep<span class="sy0">=</span><span class="st0">&quot;<span class="es0">\t</span>&quot;</span>, <a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/row.names.html"><span class="kw2">row.<span class="me1">names</span></span></a><span class="sy0">=</span><span class="nu0">1</span><span class="br0">&#41;</span>
        &nbsp;
        &nbsp;
        <span class="co1"># sort by colnames</span>
        data.<span class="me1">rpkm</span> <span class="sy0">&lt;-</span> data.<span class="me1">rpkm</span><span class="br0">&#91;</span>,<a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/order.html"><span class="kw2">order</span></a><span class="br0">&#40;</span><a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/colnames.html"><span class="kw2">colnames</span></a><span class="br0">&#40;</span>data.<span class="me1">rpkm</span><span class="br0">&#41;</span><span class="br0">&#41;</span><span class="br0">&#93;</span>
        &nbsp;
        &nbsp;
        librariesName <span class="sy0">&lt;-</span> <a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/list.html"><span class="kw2">list</span></a><span class="br0">&#40;</span>
        cop_D <span class="sy0">=</span> <a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/c.html"><span class="kw2">c</span></a><span class="br0">&#40;</span><span class="st0">&quot;cop_D&quot;</span>, <span class="st0">&quot;red&quot;</span><span class="br0">&#41;</span>,
        cop_L <span class="sy0">=</span> <a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/c.html"><span class="kw2">c</span></a><span class="br0">&#40;</span><span class="st0">&quot;cop_L&quot;</span>, <span class="st0">&quot;blue&quot;</span><span class="br0">&#41;</span>,
        spa_D <span class="sy0">=</span> <a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/c.html"><span class="kw2">c</span></a><span class="br0">&#40;</span><span class="st0">&quot;spa_D&quot;</span>, <span class="st0">&quot;green&quot;</span><span class="br0">&#41;</span>,
        spa_L <span class="sy0">=</span> <a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/c.html"><span class="kw2">c</span></a><span class="br0">&#40;</span><span class="st0">&quot;spa_L&quot;</span>, <span class="st0">&quot;yellow&quot;</span><span class="br0">&#41;</span>,
        WT_D <span class="sy0">=</span> <a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/c.html"><span class="kw2">c</span></a><span class="br0">&#40;</span><span class="st0">&quot;WT_D&quot;</span>, <span class="st0">&quot;black&quot;</span><span class="br0">&#41;</span>,
        WT_L <span class="sy0">=</span> <a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/c.html"><span class="kw2">c</span></a><span class="br0">&#40;</span><span class="st0">&quot;WT_L&quot;</span>, <span class="st0">&quot;violet&quot;</span><span class="br0">&#41;</span>
        <span class="br0">&#41;</span>
        &nbsp;
        <span class="co1"># </span>
        <span class="co1"># header.ori &lt;- c(&quot;56754_WT_Naturally_3.bam.sort.fastq.unmapped.sam.sort.bam&quot;, &quot;56753_WT_Naturally_2.bam.sort.fastq.unmapped.sam.sort.bam&quot;, &quot;56752_WT_Naturally_1.bam.sort.fastq.unmapped.sam.sort.bam&quot;, &quot;56751_tt_6_days_3.bam.sort.fastq.unmapped.sam.sort.bam&quot;, &quot;56750_tt_6_days_2.bam.sort.fastq.unmapped.sam.sort.bam&quot;, &quot;56749_tt_6_days_1.bam.sort.fastq.unmapped.sam.sort.bam&quot;, &quot;56748_tt_0_days_3.bam.sort.fastq.unmapped.sam.sort.bam&quot;, &quot;56747_tt_0_days_2.bam.sort.fastq.unmapped.sam.sort.bam&quot;, &quot;56746_tt_0_days_1.bam.sort.fastq.unmapped.sam.sort.bam&quot;, &quot;56745_WT_10_days_3.bam.sort.fastq.unmapped.sam.sort.bam&quot;, &quot;56744_WT_10_days_2.bam.sort.fastq.unmapped.sam.sort.bam&quot;, &quot;56743_WT_10_days_1.bam.sort.fastq.unmapped.sam.sort.bam&quot;, &quot;56742_WT_6_days_3.bam.sort.fastq.unmapped.sam.sort.bam&quot;, &quot;56741_WT_6_days_2.bam.sort.fastq.unmapped.sam.sort.bam&quot;, &quot;56740_WT_6_days_1.bam.sort.fastq.unmapped.sam.sort.bam&quot;, &quot;56739_WT_0_days_3.bam.sort.fastq.unmapped.sam.sort.bam&quot;, &quot;56738_WT_0_days_2.bam.sort.fastq.unmapped.sam.sort.bam&quot;, &quot;56737_WT_0_days_1.bam.sort.fastq.unmapped.sam.sort.bam&quot;, &quot;56736_tt_T1_tt_6d_3.bam.sort.fastq.unmapped.sam.sort.bam&quot;, &quot;56735_tt_T1_tt_6d_2.bam.sort.fastq.unmapped.sam.sort.bam&quot;, &quot;56734_tt_T1_tt_6d_1.bam.sort.fastq.unmapped.sam.sort.bam&quot;, &quot;56733_tt_T1_tt_0d_3.bam.sort.fastq.unmapped.sam.sort.bam&quot;, &quot;56732_tt_T1_tt_0d_2.bam.sort.fastq.unmapped.sam.sort.bam&quot;, &quot;56731_tt_T1_tt_0d_1.bam.sort.fastq.unmapped.sam.sort.bam&quot;, &quot;56730_tt_T1_tt_0d_3.bam.sort.fastq.unmapped.sam.sort.bam&quot;, &quot;56729_tt_T1_tt_0d_2.bam.sort.fastq.unmapped.sam.sort.bam&quot;, &quot;56728_tt_T1_tt_0d_1.bam.sort.fastq.unmapped.sam.sort.bam&quot;, &quot;56727_WT_T1_NA_3.bam.sort.fastq.unmapped.sam.sort.bam&quot;, &quot;56726_WT_T1_NA_2.bam.sort.fastq.unmapped.sam.sort.bam&quot;, &quot;56725_WT_T1_NA_1.bam.sort.fastq.unmapped.sam.sort.bam&quot;, &quot;56724_WT_T1_WT_0d_3.bam.sort.fastq.unmapped.sam.sort.bam&quot;, &quot;56723_WT_T1_WT_0d_2.bam.sort.fastq.unmapped.sam.sort.bam&quot;, &quot;56722_WT_T1_WT_0d_1.bam.sort.fastq.unmapped.sam.sort.bam&quot;, &quot;56721_WT_T1_WT_10d_3.bam.sort.fastq.unmapped.sam.sort.bam&quot;, &quot;56720_WT_T1_WT_10d_2.bam.sort.fastq.unmapped.sam.sort.bam&quot;, &quot;56719_WT_T1_WT_10d_1.bam.sort.fastq.unmapped.sam.sort.bam&quot;, &quot;56718_WT_T1_WT_0d_3.bam.sort.fastq.unmapped.sam.sort.bam&quot;, &quot;56717_WT_T1_WT_0d_2.bam.sort.fastq.unmapped.sam.sort.bam&quot;, &quot;56716_WT_T1_WT_0d_1.bam.sort.fastq.unmapped.sam.sort.bam&quot;, &quot;56715_WT_T1_WT_6d_3.bam.sort.fastq.unmapped.sam.sort.bam&quot;, &quot;56714_WT_T1_WT_6d_2.bam.sort.fastq.unmapped.sam.sort.bam&quot;, &quot;56713_WT_T1_WT_6d_1.bam.sort.fastq.unmapped.sam.sort.bam&quot;, &quot;56712_WT_T1_WT_0d_3.bam.sort.fastq.unmapped.sam.sort.bam&quot;, &quot;56711_WT_T1_WT_0d_2.bam.sort.fastq.unmapped.sam.sort.bam&quot;, &quot;56710_WT_T1_WT_0d_1.bam.sort.fastq.unmapped.sam.sort.bam&quot;, &quot;56709_WT_T1_WT_0d_3.bam.sort.fastq.unmapped.sam.sort.bam&quot;, &quot;56708_WT_T1_WT_0d_2.bam.sort.fastq.unmapped.sam.sort.bam&quot;, &quot;56707_WT_T1_WT_0d_1.bam.sort.fastq.unmapped.sam.sort.bam&quot;, &quot;56706_WT_T1_tt_0d_3.bam.sort.fastq.unmapped.sam.sort.bam&quot;, &quot;56705_WT_T1_tt_0d_2.bam.sort.fastq.unmapped.sam.sort.bam&quot;, &quot;56704_WT_T1_tt_0d_1.bam.sort.fastq.unmapped.sam.sort.bam&quot;)</span>
        <span class="co1"># header.new &lt;- c(&quot;T17_Dry_Naturally_Freezedryseed&quot;, &quot;T17_Dry_Naturally_Freezedryseed.1&quot;, &quot;T17_Dry_Naturally_Freezedryseed.2&quot;, &quot;T16_Dry_6days_Freezeafter6dageing&quot;, &quot;T16_Dry_6days_Freezeafter6dageing.1&quot;, &quot;T16_Dry_6days_Freezeafter6dageing.2&quot;, &quot;T15_Dry_0days_Freezedryseed&quot;, &quot;T15_Dry_0days_Freezedryseed.1&quot;, &quot;T15_Dry_0days_Freezedryseed.2&quot;, &quot;T14_Dry_10days_Freezeafter10dageing&quot;, &quot;T14_Dry_10days_Freezeafter10dageing.1&quot;, &quot;T14_Dry_10days_Freezeafter10dageing.2&quot;, &quot;T13_Dry_6days_Freezeafter6dageing&quot;, &quot;T13_Dry_6days_Freezeafter6dageing.1&quot;, &quot;T13_Dry_6days_Freezeafter6dageing.2&quot;, &quot;T12_Dry_0days_Freezedryseed&quot;, &quot;T12_Dry_0days_Freezedryseed.1&quot;, &quot;T12_Dry_0days_Freezedryseed.2&quot;, &quot;T11_Imbibe_6days_12h&quot;, &quot;T11_Imbibe_6days_12h.1&quot;, &quot;T11_Imbibe_6days_12h.2&quot;, &quot;T10_Imbibe_6days_5h&quot;, &quot;T10_Imbibe_6days_5h.1&quot;, &quot;T10_Imbibe_6days_5h.2&quot;, &quot;T9_Imbibe_0dyas_5h&quot;, &quot;T9_Imbibe_0dyas_5h.1&quot;, &quot;T9_Imbibe_0dyas_5h.2&quot;, &quot;T8_Imbibe_Naturally_47h&quot;, &quot;T8_Imbibe_Naturally_47h.1&quot;, &quot;T8_Imbibe_Naturally_47h.2&quot;, &quot;T7_Imbibe_Naturally_24h&quot;, &quot;T7_Imbibe_Naturally_24h.1&quot;, &quot;T7_Imbibe_Naturally_24h.2&quot;, &quot;T6_Imbibe_10days_72h&quot;, &quot;T6_Imbibe_10days_72h.1&quot;, &quot;T6_Imbibe_10days_72h.2&quot;, &quot;T5_Imbibe_10days_24h&quot;, &quot;T5_Imbibe_10days_24h.1&quot;, &quot;T5_Imbibe_10days_24h.2&quot;, &quot;T4_Imbibe_6days_47h&quot;, &quot;T4_Imbibe_6days_47h.1&quot;, &quot;T4_Imbibe_6days_47h.2&quot;, &quot;T3_Imbibe_6days_24h&quot;, &quot;T3_Imbibe_6days_24h.1&quot;, &quot;T3_Imbibe_6days_24h.2&quot;, &quot;T2_Imbibe_0days_24h&quot;, &quot;T2_Imbibe_0days_24h.1&quot;, &quot;T2_Imbibe_0days_24h.2&quot;, &quot;T1_Imbibe_0days_5h&quot;, &quot;T1_Imbibe_0days_5h.1&quot;, &quot;T1_Imbibe_0days_5h.2&quot;)</span>
        <span class="co1"># </span>
        <span class="co1"># header.new &lt;- header.new[order(header.ori)]</span>
        <span class="co1"># header.ori &lt;- header.ori[order(header.ori)]</span>
        <span class="co1"># </span>
        <span class="co1"># col.header &lt;- header.new</span>
        <span class="co1"># </span>
        <span class="co1"># colnames(data.rpkm) &lt;- col.header</span>
        &nbsp;
        <a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/library.html"><span class="kw2">library</span></a><span class="br0">&#40;</span><span class="st0">&quot;DESeq2&quot;</span><span class="br0">&#41;</span>
        <a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/library.html"><span class="kw2">library</span></a><span class="br0">&#40;</span><span class="st0">&quot;ggplot2&quot;</span><span class="br0">&#41;</span>
        <a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/library.html"><span class="kw2">library</span></a><span class="br0">&#40;</span><span class="st0">&quot;RColorBrewer&quot;</span><span class="br0">&#41;</span>
        <a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/library.html"><span class="kw2">library</span></a><span class="br0">&#40;</span><span class="st0">&quot;pheatmap&quot;</span><span class="br0">&#41;</span>
        <a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/library.html"><span class="kw2">library</span></a><span class="br0">&#40;</span><span class="st0">&quot;BiocGenerics&quot;</span><span class="br0">&#41;</span>
        <a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/library.html"><span class="kw2">library</span></a><span class="br0">&#40;</span><span class="st0">&quot;rgl&quot;</span><span class="br0">&#41;</span>
        <a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/library.html"><span class="kw2">library</span></a><span class="br0">&#40;</span><span class="st0">&quot;magick&quot;</span><span class="br0">&#41;</span>
        <a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/library.html"><span class="kw2">library</span></a><span class="br0">&#40;</span><span class="st0">&quot;sjmisc&quot;</span><span class="br0">&#41;</span>
        &nbsp;
        &nbsp;
        <span class="co1">################### running ######################</span>
        <span class="co1">### PCA RPKM ###</span>
        &nbsp;
        <a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/set.seed.html"><span class="kw2">set.<span class="me1">seed</span></span></a><span class="br0">&#40;</span><span class="nu0">0</span><span class="br0">&#41;</span>
        &nbsp;
        data.<span class="me1">inv</span> <span class="sy0">&lt;-</span> <a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/t.html"><span class="kw2">t</span></a><span class="br0">&#40;</span>data.<span class="me1">rpkm</span><span class="br0">&#41;</span>
        data.<span class="me1">dist</span> <span class="sy0">&lt;-</span><a href="http://stat.ethz.ch/R-manual/R-devel/library/stats/html/dist.html"><span class="kw7">dist</span></a><span class="br0">&#40;</span>data.<span class="me1">inv</span>, method<span class="sy0">=</span><span class="st0">&quot;euclidean&quot;</span><span class="br0">&#41;</span> <span class="co1"># &quot;euclidean&quot;, &quot;maximum&quot;, &quot;manhattan&quot;, &quot;canberra&quot;, &quot;binary&quot; or &quot;minkowski&quot;</span>
        data.<span class="me1">dist</span>.<span class="me1">hc</span> <span class="sy0">&lt;-</span> <a href="http://stat.ethz.ch/R-manual/R-devel/library/stats/html/hclust.html"><span class="kw7">hclust</span></a><span class="br0">&#40;</span>data.<span class="me1">dist</span>,method<span class="sy0">=</span><span class="st0">&quot;ward.D2&quot;</span><span class="br0">&#41;</span>
        data.<span class="me1">dist</span>.<span class="me1">pca</span> <span class="sy0">&lt;-</span><a href="http://stat.ethz.ch/R-manual/R-devel/library/stats/html/princomp.html"><span class="kw7">princomp</span></a><span class="br0">&#40;</span>data.<span class="me1">dist</span>,<a href="http://stat.ethz.ch/R-manual/R-devel/library/stats/html/cor.html"><span class="kw7">cor</span></a><span class="sy0">=</span><a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/T.html"><span class="kw2">T</span></a><span class="br0">&#41;</span>
        &nbsp;
        pc1 <span class="sy0">&lt;-</span> data.<span class="me1">dist</span>.<span class="me1">pca</span>$scores<span class="br0">&#91;</span>,<span class="nu0">1</span><span class="br0">&#93;</span>
        pc2 <span class="sy0">&lt;-</span> data.<span class="me1">dist</span>.<span class="me1">pca</span>$scores<span class="br0">&#91;</span>,<span class="nu0">2</span><span class="br0">&#93;</span>
        pc3 <span class="sy0">&lt;-</span> data.<span class="me1">dist</span>.<span class="me1">pca</span>$scores<span class="br0">&#91;</span>,<span class="nu0">3</span><span class="br0">&#93;</span>
        &nbsp;
        <span class="co1"># create data frame for pc1 pc2 pc3</span>
        data.<span class="me1">dist</span>.<span class="me1">pca</span>.<span class="me1">frame</span> <span class="sy0">=</span> <a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/data.frame.html"><span class="kw2">data.<span class="me1">frame</span></span></a><span class="br0">&#40;</span>pc1,pc2,pc3<span class="br0">&#41;</span>
        <a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/rownames.html"><span class="kw2">rownames</span></a><span class="br0">&#40;</span>data.<span class="me1">dist</span>.<span class="me1">pca</span>.<span class="me1">frame</span><span class="br0">&#41;</span> <span class="sy0">&lt;-</span> <a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/names.html"><span class="kw2">names</span></a><span class="br0">&#40;</span>data.<span class="me1">dist</span>.<span class="me1">pca</span>$scale<span class="br0">&#41;</span>
        <a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/colnames.html"><span class="kw2">colnames</span></a><span class="br0">&#40;</span>data.<span class="me1">dist</span>.<span class="me1">pca</span>.<span class="me1">frame</span><span class="br0">&#41;</span> <span class="sy0">&lt;-</span> <a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/c.html"><span class="kw2">c</span></a><span class="br0">&#40;</span><span class="st0">&quot;pc1&quot;</span>,<span class="st0">&quot;pc2&quot;</span>,<span class="st0">&quot;pc3&quot;</span><span class="br0">&#41;</span>
        &nbsp;
        condition.<span class="me1">values</span> <span class="sy0">&lt;-</span> <a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/c.html"><span class="kw2">c</span></a><span class="br0">&#40;</span><span class="br0">&#41;</span>
        condition.<span class="me1">values</span>.<span class="me1">color</span> <span class="sy0">&lt;-</span> <a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/c.html"><span class="kw2">c</span></a><span class="br0">&#40;</span><span class="br0">&#41;</span>
        &nbsp;
        &nbsp;
        <a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/for.html"><span class="kw2">for</span></a><span class="br0">&#40;</span>a <span class="kw1">in</span> <a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/colnames.html"><span class="kw2">colnames</span></a><span class="br0">&#40;</span>data.<span class="me1">rpkm</span><span class="br0">&#41;</span><span class="br0">&#41;</span> <span class="br0">&#123;</span>
        &nbsp;
        v <span class="sy0">&lt;-</span> <a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/substr.html"><span class="kw2">substr</span></a><span class="br0">&#40;</span>a, <a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/nchar.html"><span class="kw2">nchar</span></a><span class="br0">&#40;</span>a<span class="br0">&#41;</span>, <a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/nchar.html"><span class="kw2">nchar</span></a><span class="br0">&#40;</span>a<span class="br0">&#41;</span><span class="br0">&#41;</span>
        <a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/if.html"><span class="kw2">if</span></a><span class="br0">&#40;</span>str_contains<span class="br0">&#40;</span>v, <a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/c.html"><span class="kw2">c</span></a><span class="br0">&#40;</span><span class="nu0">1</span>,<span class="nu0">2</span>,<span class="nu0">3</span>,<span class="nu0">4</span>,<span class="nu0">5</span>,<span class="nu0">6</span>,<span class="nu0">7</span>,<span class="nu0">8</span>,<span class="nu0">9</span>,<span class="nu0">0</span><span class="br0">&#41;</span>, logic <span class="sy0">=</span> <span class="st0">&quot;or&quot;</span><span class="br0">&#41;</span><span class="br0">&#41;</span> <span class="br0">&#123;</span>
        <a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/if.html"><span class="kw2">if</span></a> <span class="br0">&#40;</span><a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/substr.html"><span class="kw2">substr</span></a><span class="br0">&#40;</span><a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/substr.html"><span class="kw2">substr</span></a><span class="br0">&#40;</span>a, <span class="nu0">1</span>, <a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/nchar.html"><span class="kw2">nchar</span></a><span class="br0">&#40;</span>a<span class="br0">&#41;</span><span class="sy0">-</span><span class="nu0">2</span><span class="br0">&#41;</span>, <a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/nchar.html"><span class="kw2">nchar</span></a><span class="br0">&#40;</span><a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/substr.html"><span class="kw2">substr</span></a><span class="br0">&#40;</span>a, <span class="nu0">1</span>, <a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/nchar.html"><span class="kw2">nchar</span></a><span class="br0">&#40;</span>a<span class="br0">&#41;</span><span class="sy0">-</span><span class="nu0">2</span><span class="br0">&#41;</span><span class="br0">&#41;</span>, <a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/nchar.html"><span class="kw2">nchar</span></a><span class="br0">&#40;</span><a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/substr.html"><span class="kw2">substr</span></a><span class="br0">&#40;</span>a, <span class="nu0">1</span>, <a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/nchar.html"><span class="kw2">nchar</span></a><span class="br0">&#40;</span>a<span class="br0">&#41;</span><span class="sy0">-</span><span class="nu0">2</span><span class="br0">&#41;</span><span class="br0">&#41;</span><span class="br0">&#41;</span> <span class="sy0">==</span> <span class="st0">&quot;.&quot;</span><span class="br0">&#41;</span> <span class="br0">&#123;</span>
        n <span class="sy0">&lt;-</span> <a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/substr.html"><span class="kw2">substr</span></a><span class="br0">&#40;</span>a, <span class="nu0">1</span>, <a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/nchar.html"><span class="kw2">nchar</span></a><span class="br0">&#40;</span>a<span class="br0">&#41;</span><span class="sy0">-</span><span class="nu0">3</span><span class="br0">&#41;</span>
        <span class="br0">&#125;</span> <span class="kw1">else</span> <span class="br0">&#123;</span>
        n <span class="sy0">&lt;-</span> <a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/substr.html"><span class="kw2">substr</span></a><span class="br0">&#40;</span>a, <span class="nu0">1</span>, <a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/nchar.html"><span class="kw2">nchar</span></a><span class="br0">&#40;</span>a<span class="br0">&#41;</span><span class="sy0">-</span><span class="nu0">2</span><span class="br0">&#41;</span>
        <span class="br0">&#125;</span>
        &nbsp;
        <span class="br0">&#125;</span> <span class="kw1">else</span> <span class="br0">&#123;</span>
        n <span class="sy0">&lt;-</span> a
        &nbsp;
        <span class="br0">&#125;</span>
        condition.<span class="me1">values</span> <span class="sy0">&lt;-</span> <a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/c.html"><span class="kw2">c</span></a><span class="br0">&#40;</span>condition.<span class="me1">values</span>, librariesName<span class="br0">&#91;</span>n<span class="br0">&#93;</span><span class="br0">&#91;</span><span class="br0">&#91;</span><span class="nu0">1</span><span class="br0">&#93;</span><span class="br0">&#93;</span><span class="br0">&#91;</span><span class="nu0">1</span><span class="br0">&#93;</span><span class="br0">&#41;</span>
        condition.<span class="me1">values</span>.<span class="me1">color</span> <span class="sy0">&lt;-</span> <a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/c.html"><span class="kw2">c</span></a><span class="br0">&#40;</span>condition.<span class="me1">values</span>.<span class="me1">color</span>, librariesName<span class="br0">&#91;</span>n<span class="br0">&#93;</span><span class="br0">&#91;</span><span class="br0">&#91;</span><span class="nu0">1</span><span class="br0">&#93;</span><span class="br0">&#93;</span><span class="br0">&#91;</span><span class="nu0">2</span><span class="br0">&#93;</span><span class="br0">&#41;</span>
        <span class="br0">&#125;</span>
        &nbsp;
        &nbsp;
        data.<span class="me1">dist</span>.<span class="me1">pca</span>.<span class="me1">frame</span><span class="br0">&#91;</span><span class="st0">&quot;tissue&quot;</span><span class="br0">&#93;</span> <span class="sy0">&lt;-</span> condition.<span class="me1">values</span>
        data.<span class="me1">dist</span>.<span class="me1">pca</span>.<span class="me1">frame</span><span class="br0">&#91;</span><span class="st0">&quot;color&quot;</span><span class="br0">&#93;</span> <span class="sy0">&lt;-</span> condition.<span class="me1">values</span>.<span class="me1">color</span>
        data.<span class="me1">dist</span>.<span class="me1">pca</span>.<span class="me1">frame</span><span class="br0">&#91;</span><span class="st0">&quot;name&quot;</span><span class="br0">&#93;</span> <span class="sy0">&lt;-</span> <a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/names.html"><span class="kw2">names</span></a><span class="br0">&#40;</span>data.<span class="me1">dist</span>.<span class="me1">pca</span>$scale<span class="br0">&#41;</span>
        <a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/attr.html"><span class="kw2">attr</span></a><span class="br0">&#40;</span>data.<span class="me1">dist</span>.<span class="me1">pca</span>.<span class="me1">frame</span>, <span class="st0">&quot;percentVar&quot;</span><span class="br0">&#41;</span> <span class="sy0">&lt;-</span> <span class="br0">&#40;</span>data.<span class="me1">dist</span>.<span class="me1">pca</span>$sdev<span class="br0">&#41;</span><span class="sy0">^</span><span class="nu0">2</span> <span class="sy0">/</span> <a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/sum.html"><span class="kw2">sum</span></a><span class="br0">&#40;</span>data.<span class="me1">dist</span>.<span class="me1">pca</span>$sdev<span class="sy0">^</span><span class="nu0">2</span><span class="br0">&#41;</span> <span class="co1"># cumsum()</span>
        &nbsp;
        <span class="co1"># simple plot</span>
        <a href="http://stat.ethz.ch/R-manual/R-devel/library/grDevices/html/png.html"><span class="kw5">png</span></a><span class="br0">&#40;</span>filename<span class="sy0">=</span>paste0<span class="br0">&#40;</span>saveat, <span class="st0">&quot;/HC_RPKM_normalized.png&quot;</span><span class="br0">&#41;</span><span class="br0">&#41;</span>
        <a href="http://stat.ethz.ch/R-manual/R-devel/library/graphics/html/plot.html"><span class="kw4">plot</span></a><span class="br0">&#40;</span>data.<span class="me1">dist</span>.<span class="me1">hc</span><span class="br0">&#41;</span> <span class="co1"># hc plot</span>
        <a href="http://stat.ethz.ch/R-manual/R-devel/library/grDevices/html/dev.off.html"><span class="kw5">dev.<span class="me1">off</span></span></a><span class="br0">&#40;</span><span class="br0">&#41;</span>
        <a href="http://stat.ethz.ch/R-manual/R-devel/library/grDevices/html/png.html"><span class="kw5">png</span></a><span class="br0">&#40;</span>filename<span class="sy0">=</span>paste0<span class="br0">&#40;</span>saveat, <span class="st0">&quot;/PCA_variance_RPKM_normalized.png&quot;</span><span class="br0">&#41;</span><span class="br0">&#41;</span>
        <a href="http://stat.ethz.ch/R-manual/R-devel/library/graphics/html/plot.html"><span class="kw4">plot</span></a><span class="br0">&#40;</span>data.<span class="me1">dist</span>.<span class="me1">pca</span><span class="br0">&#41;</span> <span class="co1"># variances; var(data.dist.pca$sdev[1:9])</span>
        <a href="http://stat.ethz.ch/R-manual/R-devel/library/grDevices/html/dev.off.html"><span class="kw5">dev.<span class="me1">off</span></span></a><span class="br0">&#40;</span><span class="br0">&#41;</span>
        <span class="co1"># get the parcent variation</span>
        percentVar <span class="sy0">&lt;-</span> <a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/round.html"><span class="kw2">round</span></a><span class="br0">&#40;</span><span class="nu0">100</span> <span class="sy0">*</span> <a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/attr.html"><span class="kw2">attr</span></a><span class="br0">&#40;</span>data.<span class="me1">dist</span>.<span class="me1">pca</span>.<span class="me1">frame</span>, <span class="st0">&quot;percentVar&quot;</span><span class="br0">&#41;</span><span class="br0">&#41;</span>
        &nbsp;
        <span class="co1"># 3d plot</span>
        plot3d<span class="br0">&#40;</span>pc1, pc2, pc3,
        type <span class="sy0">=</span> <span class="st0">&quot;s&quot;</span>, <span class="co1"># p, s, l, h, n</span>
        <span class="co1">#pch = c(1:3),</span>
        <a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/col.html"><span class="kw2">col</span></a> <span class="sy0">=</span> condition.<span class="me1">values</span>.<span class="me1">color</span>,
        size <span class="sy0">=</span> <span class="nu0">1</span>,
        xlab <span class="sy0">=</span> paste0<span class="br0">&#40;</span><span class="st0">&quot;PC1: &quot;</span>,percentVar<span class="br0">&#91;</span><span class="nu0">1</span><span class="br0">&#93;</span>,<span class="st0">&quot;% variance&quot;</span><span class="br0">&#41;</span>,
        ylab <span class="sy0">=</span> paste0<span class="br0">&#40;</span><span class="st0">&quot;PC2: &quot;</span>,percentVar<span class="br0">&#91;</span><span class="nu0">2</span><span class="br0">&#93;</span>,<span class="st0">&quot;% variance&quot;</span><span class="br0">&#41;</span>,
        zlab <span class="sy0">=</span> paste0<span class="br0">&#40;</span><span class="st0">&quot;PC3: &quot;</span>,percentVar<span class="br0">&#91;</span><span class="nu0">3</span><span class="br0">&#93;</span>,<span class="st0">&quot;% variance&quot;</span><span class="br0">&#41;</span>,
        cex <span class="sy0">=</span> <span class="nu0">2</span>,
        main <span class="sy0">=</span> <span class="st0">&quot;&quot;</span>, <span class="co1"># -&gt; princomp&quot;,</span>
        <span class="br0">&#41;</span>
        &nbsp;
        <span class="co1"># shift &lt;- matrix(4, 4, 4, byrow = TRUE)</span>
        <span class="co1"># text3d(shift,texts=1:3)</span>
        grid3d<span class="br0">&#40;</span><a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/c.html"><span class="kw2">c</span></a><span class="br0">&#40;</span><span class="st0">&quot;x&quot;</span>, <span class="st0">&quot;y&quot;</span>, <span class="st0">&quot;z&quot;</span><span class="br0">&#41;</span><span class="br0">&#41;</span>
        &nbsp;
        <span class="co1">## add legend</span>
        legend3d<span class="br0">&#40;</span><span class="st0">&quot;right&quot;</span>, <a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/unique.html"><span class="kw2">unique</span></a><span class="br0">&#40;</span>condition.<span class="me1">values</span><span class="br0">&#41;</span>, pch <span class="sy0">=</span> <span class="nu0">19</span>, <a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/col.html"><span class="kw2">col</span></a> <span class="sy0">=</span> <a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/unique.html"><span class="kw2">unique</span></a><span class="br0">&#40;</span>condition.<span class="me1">values</span>.<span class="me1">color</span><span class="br0">&#41;</span><span class="br0">&#41;</span>
        &nbsp;
        <span class="co1">#### video #####</span>
        M <span class="sy0">&lt;-</span> par3d<span class="br0">&#40;</span><span class="st0">&quot;userMatrix&quot;</span><span class="br0">&#41;</span>
        play3d<span class="br0">&#40;</span> par3dinterp<span class="br0">&#40;</span> userMatrix<span class="sy0">=</span><a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/list.html"><span class="kw2">list</span></a><span class="br0">&#40;</span>M,
        rotate3d<span class="br0">&#40;</span>M, <a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/pi.html"><span class="kw2">pi</span></a><span class="sy0">/</span><span class="nu0">2</span>, <span class="nu0">1</span>, <span class="nu0">0</span>, <span class="nu0">0</span><span class="br0">&#41;</span>,
        rotate3d<span class="br0">&#40;</span>M, <a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/pi.html"><span class="kw2">pi</span></a><span class="sy0">/</span><span class="nu0">2</span>, <span class="nu0">0</span>, <span class="nu0">1</span>, <span class="nu0">0</span><span class="br0">&#41;</span> <span class="br0">&#41;</span> <span class="br0">&#41;</span>,
        duration<span class="sy0">=</span><span class="nu0">2</span> <span class="br0">&#41;</span>
        &nbsp;
        movie3d<span class="br0">&#40;</span>spin3d<span class="br0">&#40;</span><a href="http://stat.ethz.ch/R-manual/R-devel/library/graphics/html/axis.html"><span class="kw4">axis</span></a> <span class="sy0">=</span> <a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/c.html"><span class="kw2">c</span></a><span class="br0">&#40;</span><span class="nu0">1</span>, <span class="nu0">2</span>, <span class="nu0">1</span><span class="br0">&#41;</span><span class="br0">&#41;</span>, duration <span class="sy0">=</span> <span class="nu0">5</span>,
        <a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/dir.html"><span class="kw2">dir</span></a> <span class="sy0">=</span> saveat<span class="br0">&#41;</span>
        &nbsp;
        <span class="co1">#### video end ####</span>
        &nbsp;
        <span class="co1"># pc1, pc2</span>
        <a href="http://stat.ethz.ch/R-manual/R-devel/library/grDevices/html/png.html"><span class="kw5">png</span></a><span class="br0">&#40;</span>filename<span class="sy0">=</span>paste0<span class="br0">&#40;</span>saveat, <span class="st0">&quot;/PCA_RPKM_normalized.png&quot;</span><span class="br0">&#41;</span><span class="br0">&#41;</span>
        ggplot<span class="br0">&#40;</span>
        data.<span class="me1">dist</span>.<span class="me1">pca</span>.<span class="me1">frame</span>,
        aes<span class="br0">&#40;</span>
        pc1,
        pc2,
        color<span class="sy0">=</span>tissue<span class="br0">&#41;</span>
        <span class="br0">&#41;</span> <span class="sy0">+</span>
        geom_point<span class="br0">&#40;</span>size<span class="sy0">=</span><span class="nu0">2.5</span><span class="br0">&#41;</span> <span class="sy0">+</span>
        xlab<span class="br0">&#40;</span>
        paste0<span class="br0">&#40;</span><span class="st0">&quot;PC1: &quot;</span>,percentVar<span class="br0">&#91;</span><span class="nu0">1</span><span class="br0">&#93;</span>,<span class="st0">&quot;% variance&quot;</span><span class="br0">&#41;</span>
        <span class="br0">&#41;</span> <span class="sy0">+</span>
        ylab<span class="br0">&#40;</span>
        paste0<span class="br0">&#40;</span><span class="st0">&quot;PC2: &quot;</span>,percentVar<span class="br0">&#91;</span><span class="nu0">2</span><span class="br0">&#93;</span>,<span class="st0">&quot;% variance&quot;</span><span class="br0">&#41;</span>
        <span class="br0">&#41;</span> <span class="sy0">+</span>
        <span class="co1">#theme() + #, face=&quot;bold&quot;</span>
        scale_colour_manual<span class="br0">&#40;</span>
        values<span class="sy0">=</span> <a href="http://stat.ethz.ch/R-manual/R-devel/library/base/html/c.html"><span class="kw2">c</span></a><span class="br0">&#40;</span><span class="st0">&quot;red&quot;</span>, <span class="st0">&quot;blue&quot;</span>, <span class="st0">&quot;green&quot;</span>, <span class="st0">&quot;yellow&quot;</span>, <span class="st0">&quot;black&quot;</span>, <span class="st0">&quot;violet&quot;</span><span class="br0">&#41;</span> <span class="co1"># dodgerblue3</span>
        <span class="br0">&#41;</span> <span class="sy0">+</span>
        ggtitle<span class="br0">&#40;</span><span class="st0">&quot;PCA of all samples (RPKM normalized)&quot;</span><span class="br0">&#41;</span> <span class="sy0">+</span>
        theme<span class="br0">&#40;</span>
        plot.<span class="me1">title</span> <span class="sy0">=</span> element_text<span class="br0">&#40;</span>lineheight<span class="sy0">=</span>.8<span class="br0">&#41;</span>,
        panel.<span class="me1">background</span> <span class="sy0">=</span> element_rect<span class="br0">&#40;</span>fill <span class="sy0">=</span> <span class="st0">&quot;gray95&quot;</span><span class="br0">&#41;</span>
        <span class="br0">&#41;</span>
        <a href="http://stat.ethz.ch/R-manual/R-devel/library/grDevices/html/dev.off.html"><span class="kw5">dev.<span class="me1">off</span></span></a><span class="br0">&#40;</span><span class="br0">&#41;</span></pre>
        </dd></dl>
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        <div class="docInfo"><bdi>personal/haasf/2021/madland/rnaseqhoecker/3d_pca_plot_hoecker_20210527.r.txt</bdi> · Last modified: 2021/06/01 12:22 by <bdi>Fabian Haas</bdi></div>
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