title: Small problem of legend color in PCA, is it a bug or my script miswriting?
body: <p>I ran a PCA and customized it via ggplot (on DESeq2 RNAseq data). Everything looks well excepted the legend that appears all black for the 2 genotypes (see the Genotype legend on right of the picture) while the PCA itself looks great (genotype 1 is well colored in green and genotype 2 colored in red, both individualy shaped with a dark border line). I have tried many writings but I am stucked concerning the legend looking. Thanks for help.</p>
  
  <p>The script :</p>
  
  <pre><code>############# PCA
  names&lt;-colnames(rld)
  
  pcaData &lt;- plotPCA(rld, intgroup=c("Genotype", "Treatment"), returnData=TRUE)
  
  percentVar &lt;- round(100 * attr(pcaData, "percentVar"))
  
  
  ggplot(pcaData, aes(PC1, PC2, color=Genotype, shape=Treatment, fill=Genotype, label=names)) +
    geom_point(size=3) +
    ggtitle("PCA | Prunus") +
    theme(legend.position = "right") +
    xlab(paste0("PC1: ",percentVar[1],"% variance")) +
    ylab(paste0("PC2: ",percentVar[2],"% variance")) + 
    coord_cartesian()+
    scale_shape_manual(values=c(21,23))+
    scale_color_manual(values = c("#000000", "#000000")) +
    scale_fill_manual(values = c("#78D212", "#C12D0D")) +
    stat_ellipse(type = "norm", geom="polygon", level=0.8,alpha=0.2)+
    theme(
      axis.line = element_line(colour = "black", size = 1, linetype = "solid"),
      panel.background = element_rect(fill = "white", colour = "black", size = 2, linetype = "solid"),
      panel.grid.major = element_line(colour ="grey", size = , linetype = "dashed"),
      panel.grid.minor = element_line(colour ="black", size = , linetype = "dashed")
      )
  </code></pre>
  
  <p>The graph (see the 2 black circles in the genotype legend (instead of expected green and red + black line)):</p>
  
  <p><img src="https://i.stack.imgur.com/h3Dn2.jpg" alt="Link"></p>
  
  <p>Below are some tests I have done according to comments.</p>
  
  <p><a href="https://i.stack.imgur.com/aRQqh.jpg" rel="nofollow noreferrer">Link</a></p>
  
  <p>Thanks for your help.</p>