Hello everyone, I hope everyone of you had some fun in this summer time. I am back to work and I'm having some issue with DEP tool for proteomic. I have to make a PCA plot, and for some reason I don't see my all my samples in the plot but only some of them. When I run the code
plot_pca(dep, x = 1, y = 2, n = 500, point_size = 4,plot = T)
the plot is this:
instead of having all of this samples represented below
sample PC1 PC2 condition replicate
1 T_ALL_1 -15.624146 34.899837 T_ALL 1
2 T_ALL_2 -22.013036 30.657545 T_ALL 2
3 Leukocyte_1 27.041054 2.388217 Leukocyte 1
4 Leukocyte_2 27.540329 2.262688 Leukocyte 2
5 Leukocyte_3 13.255157 16.520955 Leukocyte 3
6 Leukocyte_4 28.858711 16.422760 Leukocyte 4
7 Leukocyte_5 -4.799837 9.693203 Leukocyte 5
8 Leukocyte_6 -5.449344 -26.052015 Leukocyte 6
9 Leukocyte_7 -5.089086 -19.024295 Leukocyte 7
10 Leukocyte_8 -4.722665 -25.082722 Leukocyte 8
11 Leukocyte_9 24.306572 10.368625 Leukocyte 9
12 Leukocyte_10 41.809260 -15.398383 Leukocyte 10
13 Leukocyte_11 39.288471 -11.986414 Leukocyte 11
14 Leukocyte_12 38.284847 -3.482945 Leukocyte 12
15 Thymus_1 -31.392348 -11.243681 Thymus 1
16 Thymus_2 -34.516488 -4.929370 Thymus 2
17 Thymus_3 -25.093346 20.779489 Thymus 3
18 Thymus_4 -42.765353 -8.536767 Thymus 4
19 Thymus_5 -14.625431 -5.656757 Thymus 5
20 Thymus_6 -28.877825 -8.647515 Thymus 6
21 Thymus_7 -21.969212 -11.729715 Thymus 7
22 Thymus_8 16.553716 7.777260 Thymus 8
Can somebody please help me with it?
Thank you
•
written
by
Morris_Chair
2 answers
Looks like you have more replicates than there are symbols. Just drop replicate from the indicate: plot_pca(..., indicate='condition')
Or switch to a more advanced package like PCAtools by the very active Kevin Blighe
Since you have more replicates (n=12) than default symbols, you can add ggplot scale_shape_manual(values=seq(...)) to your pca_plot function.
plot_pca(dep, x = 1, y = 2, n = 500, point_size = 4,plot = T) + scale_shape_manual(values=seq(0,11))
# OR to get more defined shapes, you can do sth like this
plot_pca(dep, x = 1, y = 2, n = 500, point_size = 4,plot = T) + scale_shape_manual(values=c(7,8,9,10,11,12,13,14,15,16,17,18))
One could probably even plot Trump's mugshot as a symbol, to be honest with you. That would make Nature without peer review.
Log in to answer this question.
Try increasing the
nvalue. The plot legend is odd - there are no shapes assigned to a majority of the replicates.