Hi,
I am trying to plot my pca in ggplot and I've manage to get something (picture attached).
My question is, How do I spread the axis scales to make it look better. This is the worst ggplot that I've ever seen! Please help me fix it.
This is my code:
b <- ggplot(pca, aes(PC1, PC2, col = spp, shape = loc)) + geom_point(size = 3)
b <- b + scale_colour_manual(values = c("red", "blue", "green", "yellow", "brown","purple"))
b <- b + coord_equal() + theme_light()
b + xlab(paste0("PC1 (", signif(pve$pve[1], 3), "%)")) + ylab(paste0("PC2 (", signif(pve$pve[2], 3), "%)"))
image: https://ibb.co/XLp4hCk
P.S: I'm new to R and very eager to learn. I tried setting x and y lim (scale_x_continuous, expand_limits, coord_cartesian etc.)
UPDATE: Here are the first few lines of data, as per request;
structure(list(ind = c("IID", "\"$i\"", "filtered_seq1trimq10_LHA_EU21_1.final_snps_\"$i\"",
"filtered_seq1trimq10_Tur09_1.final_snps_\"$i\"", "filtered_seq1trimq10_LHA_EU20_1.final_snps_\"$i\"",
"filtered_seq1trimq10_LHA_AS201_1.final_snps_\"$i\""), PC1 = c("PC1",
"0.0915729", "0.0946641", "0.0633914", "0.0951517", "-0.235733"
), PC2 = c("PC2", "0.040677", "0.0470369", "-0.0144166", "0.0490094",
"0.100445"),
•
written
by
niyomiw88 •
It seems that PC1 and PC2 are factors. Change them to numeric and it will work :
pca$PC1 <- as.numeric(as.character(pca$PC1))
pca$PC2 <- as.numeric(as.character(pca$PC2))
Also to spread the axis in ggplot you can use scale_x_continuous() and scale_y_continous()
Example :
# dummy data
dat <- data.frame(x=1:10,y=1:10)
# plot without axis spreading
dat %>%
ggplot(aes(x=x,y=y)) +
geom_point()
# plot with axis spreading : x-axis [-5,15] ; y-axix[-2,12]
dat %>%
ggplot(aes(x=x,y=y)) +
geom_point() +
scale_x_continuous(limits = c(-5,15)) +
scale_y_continuous(limits = c(-2,12))
Hey, Sorry for the late reply. But your suggestion worked. Thank you so much. However, it did change the population structure. I am not sure why? All i changed is factor to numeric. I am having trouble embedding the new plot. But I will soon!
Try library(ggfortify); autoplot(pca) - that might be a good starting point. autoplot will accept a few more arguments to help customize the plot a little.
You can also add columns to the object subjected to the PCA operation that can be used to color/shape by (such as your spp and loc) Let's say that object is dat and you get pca by pca <- prcomp(dat).
You can add the spp and loc columns to dat, then
library(ggfortify)
autoplot(prcomp(dat[,!(colnames(dat) %in% c("spp", "loc"))]), color = "spp", shape = "loc", label = TRUE)
See this page for more details: https://cran.r-project.org/web/packages/ggfortify/vignettes/plot_pca.html
I really only have one species that belong to 6 geographical areas. I made an error putting "spp" on the plot above. I did give ggfortify a try but honestly, i didn't try hard enough. I can give it another try.
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Can you add some of your data to the post using
dput(head(pca))? It makes it easier for people to answer the question.Thank you for the tip. I updated my post :)
codeoption) to present your post better. You can use backticks for inline code (`text` becomestext), or select a chunk of text and use the highlighted button to format it as a code block. I've done it for you this time.Thank you so much for the helpful tips. I hardly ever post anything, because I can find answers to most of my questions here already.
Your example data is incomplete. Please post complete example data. Change the the intervals on Y-axis as they are numbers. It is not clear what is on the x-axis. If they are numbers (as y-axis values), change the interval. Why is
indcharacter vector has$iin it?PC "numbers" are not numeric:
I think you imported the data header as the 1st row, which then turned all following numeric values into character. Please share the code you have used for data import.