title: prcomp + ggbiplot : invalid 'rot' value
body: <p>I am a real beginner in programming. I previously ran a PCA without normalizing my data and using</p>
  <pre><code>pca1 &lt;- prcomp(df1[, -1792],  scale = TRUE)
  </code></pre>
  <p>where column 1792 was a non-numeric value (stages of a disease).I also filtered in this case with my 1791 &quot;golden&quot; DEGs (Differentially Expressed Genes).
  I then ran this ggbiplot code with no issue:</p>
  <pre><code>ggbiplot(pca1, groups=factor (df1$stage), alpha=1, varname.size=0.2, ellipse = TRUE, circle = TRUE, labels =row.names(df1)) +theme_bw()
  </code></pre>
  <p>but I have a very low PC1+PC2 contribution (variance explained: ~34%).</p>
  <p>I'm now trying to run a PCA after I have used the DESeq2 function</p>
  <pre><code>df2 &lt;- vst(dds, blind = FALSE) 
  </code></pre>
  <p>to normalize my data. dds comes from a function within deseq2 but what matters is that when I use</p>
  <pre><code>df2 &lt;- assay(df2)
  </code></pre>
  <p>I get a dataframe with normalized counts so then I can use the scale=F in the prcomp:</p>
  <pre><code>pca2 &lt;- prcomp(df2, scale=FALSE)
  </code></pre>
  <p>The pca runs properly but once I run the ggbiplot I get this error</p>
  <pre><code>plot &lt;- ggbiplot(pca2, groups=factor (df2$stage), alpha=1, varname.size=0.2, ellipse = TRUE, circle = TRUE, labels =row.names(df2))
  &gt; plot
  Error in validDetails.text(x) : invalid 'rot' value
  </code></pre>
  <p>The df2 has 62 rows and 18041 coumns. The column names are the genes, not filtered with the &quot;golden&quot; 1791 DEGs.</p>
  <p>Does anyone know what this issue could be?</p>
  <pre><code> dput(vstFnaflf2[1:2])
  structure(list(ENSG00000000003 = c(11.4215544074842, 11.3369519651205, 
  11.5448391216299, 11.2668610511339, 10.8654320557767, 11.4886601274776, 
  11.1553462673246, 10.8894337958264, 11.3799538821303, 11.1834947682376, 
  11.1377551871347, 10.8635788490664, 10.7571820846599, 11.2293442248949, 
  11.242436020635, 11.1190373991806, 11.4220714063675, 11.3441908169498, 
  11.1158875256387, 11.4749364557432, 11.2191249607138, 10.680739153785, 
  11.029716588235, 10.4306314563696, 11.1063383712873, 10.6729270823035, 
  10.7778905669614, 10.4691752830184, 10.9689082384651, 11.2816279203297, 
  11.0424792087751, 11.6996231284794, 11.1902799982159, 10.8527510875352, 
  11.3022219384651, 11.1458750833418, 10.8359910845809, 11.2148430328843, 
  10.9732261450675, 10.2091729321716, 11.1967880011015, 10.9659701944552, 
  10.838617541679, 11.1004203325252, 10.6932651834237, 10.5629477735197, 
  10.2605983436435, 10.4749930961273, 10.4742010629573, 9.76884707077027, 
  10.3490782724558, 10.0733457365331, 9.92868836741446, 10.5738569015904, 
  11.2038970989381, 11.2849826368472, 11.0610922087208, 10.4281519728595, 
  10.6111525987206, 11.4163114688057, 11.2237933238777, 11.3615193043112
  ), ENSG00000000005 = c(4.76699423435736, 4.68240208192305, 3.83645876209821, 
  3.83645876209821, 4.66839871345985, 4.79885068975568, 4.416012172989, 
  3.83645876209821, 5.36435617001811, 4.26063011770966, 4.53405567978961, 
  4.33533017372147, 3.83645876209821, 4.33383458328636, 3.83645876209821, 
  3.83645876209821, 4.59610823121884, 4.17207999667687, 3.83645876209821, 
  5.32000950445877, 4.39196210894947, 3.83645876209821, 3.83645876209821, 
  4.21330292986232, 4.31404327784339, 4.2226205020253, 3.83645876209821, 
  3.83645876209821, 4.25346930315269, 3.83645876209821, 3.83645876209821, 
  3.83645876209821, 5.706574065477, 4.49155709713843, 4.7605669687025, 
  4.81682091160677, 3.83645876209821, 3.83645876209821, 5.23038711339047, 
  4.9317232361801, 3.83645876209821, 3.83645876209821, 4.63880384026439, 
  3.83645876209821, 5.0817203747019, 3.83645876209821, 3.83645876209821, 
  3.83645876209821, 3.83645876209821, 3.83645876209821, 4.50626310563055, 
  4.41409771719511, 4.26279976373479, 3.83645876209821, 3.83645876209821, 
  4.2035349073738, 3.83645876209821, 3.83645876209821, 3.83645876209821, 
  4.35675165408212, 3.83645876209821, 4.17523694633528)), row.names = c(&quot;control001&quot;, 
  &quot;control002&quot;, &quot;control003&quot;, &quot;control004&quot;, &quot;control005&quot;, &quot;control006&quot;, 
  &quot;control007&quot;, &quot;control008&quot;, &quot;control009&quot;, &quot;control010&quot;, &quot;patient007&quot;, 
  &quot;patient009&quot;, &quot;patient011&quot;, &quot;patient012&quot;, &quot;patient019&quot;, &quot;patient026&quot;, 
  &quot;patient028&quot;, &quot;patient029&quot;, &quot;patient044&quot;, &quot;patient056&quot;, &quot;patient058&quot;, 
  &quot;patient059&quot;, &quot;patient070&quot;, &quot;patient073&quot;, &quot;patient081&quot;, &quot;patient085&quot;, 
  &quot;patient086&quot;, &quot;patient089&quot;, &quot;patient092&quot;, &quot;patient097&quot;, &quot;patient101&quot;, 
  &quot;patient107&quot;, &quot;patient109&quot;, &quot;patient110&quot;, &quot;patient113&quot;, &quot;patient114&quot;, 
  &quot;patient116&quot;, &quot;patient118&quot;, &quot;patient120&quot;, &quot;patient121&quot;, &quot;patient123&quot;, 
  &quot;patient129&quot;, &quot;patient131&quot;, &quot;patient132&quot;, &quot;patient137&quot;, &quot;patient139&quot;, 
  &quot;patient143&quot;, &quot;patient144&quot;, &quot;patient146&quot;, &quot;patient151&quot;, &quot;patient152&quot;, 
  &quot;patient156&quot;, &quot;patient158&quot;, &quot;patient164&quot;, &quot;patient166&quot;, &quot;patient178&quot;, 
  &quot;patient184&quot;, &quot;patient187&quot;, &quot;patient188&quot;, &quot;patient199&quot;, &quot;patient201&quot;, 
  &quot;patient206&quot;), class = &quot;data.frame&quot;)
  </code></pre>