Adding ellipse in PCAtools biplot
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Entering edit mode
M Tuhin • 0
@4ad593ce
Last seen 4 hours ago
Australia

Enter the body of text here

Hi All, I need some urgent help regrading pca analysis to show the clustering of my 13 samples based on treatment condition. I have run the code and generated a biplot which is showing the 13 points represent 13 samples but the problem is I want to draw an ellipse for 2/3 replicates under the same treatment. How can i do that? Could anyone help me in this regards?

Please help me with your experiences.

Finalized script for PCA using Bioconductor::PCAtools

Principle component analysis

Without data normalization

library(readxl)

df <- read_excel("tpp.xlsx")

colnames(df)

ta <- df[, 2:14]

ta <- as.matrix(ta)

metadata <- data.frame(row.names = colnames(ta))

metadata$Group <- rep(NA, ncol(ta))

metadata$Group[seq(1,2)] <- 'Batch 1 Control'

metadata$Group[seq(3,4)] <- 'Batch 1 P100'

metadata$Group[seq(5,7)] <- 'Batch 2 Control'

metadata$Group[seq(8,10)] <- 'Batch 2 P25'

metadata$Group[seq(11,13)] <- 'Batch 2 P100'

library(ggplot2)

library(ggrepel)

library(PCAtools)

tpp.pca <- pca(ta, metadata = metadata, scale = FALSE)

biplot(tpp.pca)

biplot(tpp.pca, pointSize = 5, lab = NULL, labSize = 4, colby = 'Group', shape = 'Group', legendPosition = 'right')

biplot(tpp.pca, pointSize = 3, lab = p$yvars, labSize = 4, colby = 'Group', shape = 'Group', legendPosition = 'right')

Adding ellipse is still not working

All of these codes are not producing ellipse

biplot(tpp.pca, pointSize = 5, lab = NULL, labSize = 4, colby = 'Group', shape = 'Group', legendPosition = 'right') + geom_point() + stat_ellipse(aes(group = 'Group'), type = "norm")

An incomplete ellipse is formed from the above code

biplot(tpp.pca, pointSize = 5, lab = NULL, labSize = 4, colby = 'Group', shape = 'Group', ellipse = TRUE, legendPosition = 'right')

Above code results in:

Too few points to create an ellipse

library(ggforce) also used (may be wrong way)

biplot(tpp.pca, pointSize = 5, lab = NULL, labSize = 4, colby = 'Group', shape = 'Group', ellipse = TRUE, legendPosition = 'right') +

ggforce::geom_mark_ellipse(aes(color = 'Group'))r

include your problematic code here with any corresponding output

please also include the results of running the following in an R session

sessionInfo( )

```

Biplot FactoMineR proteomics PCAtools ellipse • 110 views
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1
Entering edit mode
@kevin
Last seen 8 hours ago
Republic of Ireland

Hi,

Please increase the values for xlim and / or ylim.

Kind regards,

Kevin

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Entering edit mode

Hi kevin many thanks for your answer? How can I found the existing up and lower limit? If I increase these limits instead of NULL, will then the following code work?

biplot(tpp.pca, pointSize = 5, lab = NULL, labSize = 4, colby = 'Group', shape = 'Group', ellipse = TRUE, xlim = NULL, ylim = NULL legendPosition = 'right')

This is my existing graph. I want to have an ellipse around every cluster.

enter image description here

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0
Entering edit mode

Hi, you can observe the values on the current axes, and then set new limits of greater absolute values via xlim and ylim, and then re-generate the plot.

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