Adjust color of ellipse in PCA plot from DESeq2 data set
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0
Entering edit mode
thu.vo • 0
@313d375a
Last seen 11 months ago

I would like to create a PCA plot with ellipse for grouping. I have a dataset from DESeqFromHTSeqCount. I can change the color of point but could not adjust the color of ellipse. My code is below:

> #Set working directory for data
> setwd("C:/Users/t_v026/Dropbox/Atlantic salmon/New RNAseq/DEG Analysis/RawCount")
> directory <- "C:/Users/t_v026/Dropbox/Atlantic salmon/New RNAseq/DEG Analysis/RawCount/"
> sampleTableT <- read.delim("SampleTableTotal.txt", sep = "\t")
> 
> ###Create DESeqDataSet
> ddsHTSeqTotal <- DESeqDataSetFromHTSeqCount(sampleTable = sampleTableT, directory = directory, design = ~ Tissue)
Warning message:
In DESeqDataSet(se, design = design, ignoreRank) :
  some variables in design formula are characters, converting to factors
> ddsHTSeqTotal
class: DESeqDataSet 
dim: 48436 40 
metadata(1): version
assays(1): counts
rownames(48436): 1433b 1433z ... zyx zzef1
rowData names(0):
colnames(40): BC26B187 BC27N219 ... P26B180 P26N210
colData names(2): Color Tissue
> 
> 
> #Keep only read that have counts >10
> keep1 <- rowSums(counts(ddsHTSeqTotal)) >= 10
> ddsHTSeqTotal1 <- ddsHTSeqTotal[keep1,]
> ###Generation of PCA
> vsdT <- vst(ddsHTSeqTotal1,blind=FALSE)
> pltT <- ggplot(pT, aes(PC1, PC2, color = Tissue, shape = Tissue)) + 
+   geom_point(aes(color = Tissue, shape=Tissue, size=Tissue))+
+   scale_shape_manual(values=c(16, 17, 18))+
+   scale_color_manual(values=c('#FFFF00','#FF6600', '#3399FF')) +
+   scale_size_manual(values=c(2,2,3)) +
+   theme_bw() +
+   theme(axis.line = element_line(colour = "black"),
+         panel.grid.major = element_blank(),
+         panel.grid.minor = element_blank(),
+         panel.border = element_blank(),
+         panel.background = element_blank()) +
+   xlab(paste0("PC1: ", percentVarT[1], "% variance")) +
+   ylab(paste0("PC2: ", percentVarT[2], "% variance")) +
+   coord_fixed() + ylim(-40,40) +
+   stat_ellipse(aes(x=PC1,y=PC2,fill = Tissue, color = Tissue), geom = "polygon", linetype = "blank", level=0.95, alpha=0.2)
> pltT
# include your problematic code here with any corresponding output 
# please also include the results of running the following in an R session 

sessionInfo( )
![Result of PCA plot][1]

Could anyone please give me an advice? Thank you so much.

Thu

stat_ellipse DESeq2 ggplot2 • 236 views
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Entering edit mode
@james-w-macdonald-5106
Last seen 13 hours ago
United States

Questions about the tidyverse (which includes ggplot2) should probably be asked elsewhere. Or you could just do a search of say 'stat_ellipse change line color' which is my usual method when trying to navigate the tidyverse.

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