I have a dataframe called split2_data (actually a drop-leveled subset of a bigger data frame).
It contains a column “Loci”, which are factors that I want as x-axes, and several columns of y-values (note: All of these values are <=1) that I would like to plot beside one another in their respective x factor.
The dataframe
structure(list(Loci = structure(1:8, .Label = c("C485", "C487_PigTa",
"C536", "Carey", "Cool", "Coyote", "Deadpool", "Epstein"), class = "factor"),
All = structure(c(5L, 6L, 7L, 1L, 2L, 4L, 3L, 8L), .Label = c("0.0246",
"0.0352", "0.0563", "0.0646", "0.2349", "0.3242", "0.3278",
"0.6854"), class = "factor"), X1_only = structure(c(4L, 3L,
2L, 1L, 6L, 6L, 6L, 5L), .Label = c("0.0133", "0.7292", "0.8586",
"0.9377", "0.961", "1"), class = "factor"), X78_only = structure(c(7L,
6L, 4L, 5L, 8L, 3L, 1L, 2L), .Label = c("0.0018", "0.0175",
"0.4958", "0.6055", "0.7472", "0.7563", "0.825", "1"), class = "factor"),
X8_removed = structure(c(5L, 6L, 8L, 1L, 2L, 3L, 4L, 7L), .Label = c("0.0181",
"0.0348", "0.1482", "0.1706", "0.2217", "0.2602", "0.6748",
"0.7123"), class = "factor"), X8_only = structure(c(6L, 7L,
3L, 8L, 5L, 4L, 1L, 2L), .Label = c("0.1266", "0.1945", "0.4389",
"0.4496", "0.7078", "0.709", "0.8882", "1"), class = "factor"),
X7_removed = structure(c(6L, 4L, 5L, 2L, 1L, 3L, 7L, 8L), .Label = c("0.0159",
"0.02", "0.0541", "0.3232", "0.3972", "0.4226", "0.4919",
"0.5951"), class = "factor"), X7_only = structure(c(3L, 4L,
7L, 5L, 6L, 8L, 1L, 2L), .Label = c("0.0082", "0.1759", "0.4957",
"0.5248", "0.6665", "0.6789", "0.8372", "1"), class = "factor"),
X5_removed = structure(c(5L, 7L, 6L, 1L, 3L, 4L, 2L, 8L), .Label = c("0.0195",
"0.0316", "0.08", "0.1069", "0.1549", "0.395", "0.4405",
"0.6298"), class = "factor"), X5_only = structure(c(1L, 2L,
6L, 7L, 3L, 5L, 7L, 4L), .Label = c("0.0871", "0.2022", "0.3532",
"0.3677", "0.5292", "0.7602", "1"), class = "factor"), X4_removed = structure(c(8L,
4L, 7L, 2L, 3L, 5L, 1L, 6L), .Label = c("0.0188", "0.0194",
"0.0511", "0.1716", "0.1862", "0.6454", "0.661", "0.8003"
), class = "factor"), X4_only = structure(c(2L, 5L, 1L, 6L,
7L, 3L, 8L, 4L), .Label = c("0.0026", "0.0378", "0.2884",
"0.4386", "0.5116", "0.6549", "0.6928", "1"), class = "factor"),
X3_removed = structure(c(5L, 7L, 6L, 1L, 2L, 3L, 4L, 8L), .Label = c("0.0612",
"0.0627", "0.0808", "0.1636", "0.2728", "0.477", "0.5307",
"0.6506"), class = "factor"), X3_only = structure(c(8L, 1L,
7L, 2L, 4L, 6L, 3L, 5L), .Label = c("0.0225", "0.2111", "0.2471",
"0.5087", "0.6294", "0.768", "0.8263", "0.8951"), class = "factor"),
X2_removed = structure(c(4L, 5L, 6L, 3L, 7L, 2L, 1L, 8L), .Label = c("0.0526",
"0.0608", "0.0854", "0.2036", "0.3168", "0.3668", "0.413",
"0.7608"), class = "factor"), X2_only = structure(c(5L, 3L,
6L, 4L, 2L, 8L, 1L, 7L), .Label = c("-", "0.0014", "0.0949",
"0.1637", "0.1818", "0.5521", "0.8585", "1"), class = "factor"),
X1_removed = structure(c(5L, 7L, 3L, 6L, 1L, 4L, 2L, 8L), .Label = c("0.0258",
"0.031", "0.0496", "0.0676", "0.1053", "0.1439", "0.2823",
"0.5465"), class = "factor")), .Names = c("Loci", "All",
"X1_only", "X78_only", "X8_removed", "X8_only", "X7_removed",
"X7_only", "X5_removed", "X5_only", "X4_removed", "X4_only",
"X3_removed", "X3_only", "X2_removed", "X2_only", "X1_removed"
), row.names = 9:16, class = "data.frame")
I can’t think of how to do this in base R, and after some careful study of other questions here, this is the best that I can come up with:
library(reshape)
library(ggplot2)
require(ggplot2)
split2_datam<-melt(split2_data,id="Loci")
p2<- ggplot(split2_datam, aes(x =Loci, y = value, color = variable, width=.15)) + geom_bar(position="dodge") + ylab("P-value")+ geom_hline(yintercept=0.05)+ opts(axis.text.x = theme_text(angle=90, size=8)) + scale_y_discrete(breaks=seq(0,1)) + scale_fill_grey()
p2
#when I add stat="identity", the y values don't change- they just shrink relative to the x-axis
p2<- ggplot(split2_datam, aes(x =Loci, y = value, color = variable, width=.15)) + geom_bar(position="dodge", stat="identity") + ylab("P-value")+ geom_hline(yintercept=0.05)+ opts(axis.text.x = theme_text(angle=90, size=8)) + scale_y_discrete(breaks=seq(0,1)) + scale_fill_grey()
p2
The plot:
You’ll notice that the different variables are often much greater than 1. They should not be. Any idea what’s causing this/how to fix?
Other things I don’t yet know how to do/fix (perhaps this question should be cross-referenced?):
- I don’t know why the greyscale isn’t working
- I don’t know how to make the legend scale correctly with the plot
- I don’t understand why my columns have an ‘X’ appended to them (e.g. “X1_only” instead of “1_only”)
Thank you so much in advance for any suggestions!
Your data have been read in as factors, probably because there are some “-” characters mixed in with your data.
You’ll want to convert them to
NAwhen you read in your data usingna.strings = "-".