Plot factors by specific column in ggplot
Hi everyone,
I'm using DAPC to analyze the population structure of a GBS dataset. I was able to generate a table with the following:
Population Accession Assigned Membership
1 C. a jal 1 9.051345e-63
2 C. a ancho 2 1.396897e-10
3 C. b toro 3 0.000000e+00
4 C. b b37 1 0.000000e+00
5 C. c mis 1 0.000000e+00
6 C. a jal 2 9.051345e-63
7 C. a ancho 1 1.396897e-10
8 C. b toro 4 0.000000e+00
9 C. b b37 2 0.000000e+00
10 C. c mis 3 0.000000e+00
...
Then I used ggplot to plot the compoplot (Structure-like):
cap.color <- brewer.pal(n = 7, name = "Set3")
ggplot(cap.dapc, aes(x=Accession, y=Membership, fill=Assigned)) +
geom_bar(stat='identity') +
scale_fill_manual(values = cap.color) +
facet_grid(~Population, scales = "free", space = "free_x") +
theme(axis.text.x = element_text(angle = 90, hjust = 0, vjust = 0.5)) +
xlab("Accession")
That results in a plot ordered alphabetically by sample name and by population. My goal is to change the code in order to samples appear order by the Assigned category and Membership. How can I do that?
I've tried using
cap.dapc$Accession <- factor(cap.dapc$Assigned, levels = rev(unique(cap.dapc$Accession)), ordered=TRUE)
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If it is a generic order thing in ggplot2 checkout https://kohske.wordpress.com/2010/12/29/faq-how-to-order-the-factor-variables-in-ggplot2/
you are missing
cap.colorin test data and sample number. Barplot is faceted by population. Hence all your plots will be faceted by population categories (factors), in this case a, b and c. Within each population, x axis has accession and y -axis has membership. Hence you can manipulate the order of accession (x-axis) only. Is that what is required? leeandroidI've just added the color palette to my original post. You're right, I can only change the accession order. Another option would be changing the layout of the plot entirely, but I can't think of a clearer way to put it.
well, whatever you have mind, you can put it here. some one will understand it and provide a solution. That is how we learn here. leeandroid
factor every column which you want to order, then feed combination in facet_grid(), you can take help from this post
I've tried factor both Assigned and Membership but it didn't work. I'm not sure I put it correctly:
I'm not sure if my example data is clear enough for you guys to get the picture. Each accession appears Assigned 7 times and the Membership column has the probability of that assignation (which could be from 0 to 1).
Thanks for your help!