An question about PCA analysis of protein data in R
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Entering edit mode
4 months ago
741801556 • 0

I wonder know how to define the fill and colour using my data in R?

Code is as follows:

data <- read.table("G:/protomtics/20231228-QCM-Gas/20231229-QCM-Gas/data analysis/pca_data.csv",header = T, row.names = 1, sep = ",")
pca <- principal(train.scale, rotate="none")
plot(pca$values, type="b", ylab="Eigenvalues", xlab="Component")
pca.rotate <- principal(train.scale, nfactors = 2, rotate ="varimax")
pca.rotate

pca.scores <- data.frame(pca.rotate$scores)
head(pca.scores)

                 RC1         RC2
WT_1_126    56.09007  54.1052753
WT_2_127    64.48834  48.1215063
WT_3_126    64.96041   0.5308317
WT_4_127    71.08494  -4.6388461
DMD_1_128N -70.23270 -32.4267293
DMD_2_128C -68.77648 -42.3431540#

pca.scores$Sample_id <- data$Sample_id
library(ggplot2)

p1<-ggplot(pca.scores, aes(x = RC1, y = RC2,fill = Sample_id,colour = Sample_id)
Caused by error:
! Can't find a date.'Sample_id'
PCA • 541 views
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Entering edit mode

You need to post what pca.scores looks like. You're also missing a geometry to add to the plot, like geom_point().

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sorry about that. I have posted a part of the code.

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Entering edit mode
4 months ago
Mensur Dlakic ★ 27k

Your sample (first) columns has no name, and it should be named Sample_id for your code to work.

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Thanks your helping.

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