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Asked: 2026-06-05T20:34:24+00:00

This should be a pretty straightforward question. I have the following code, which forms

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This should be a pretty straightforward question. I have the following code, which forms the plot I want:

library(reshape)
library(ggplot2)
require(ggplot2)
split1_data<-structure(list(Loci = structure(1:8, .Label = c("Baez", "Blue", 
"C147", "C204", "C21", "C278_PT", "C294", "C316"), class = "factor"), 
    All = c(0.3357, 0.4166, 0.0242, 0.9708, 0.4518, 0.0666, 0, 
    0.5925), X1_only = c(0.4758, 0.3188, 0.1465, 0.3209, 1, 0.0278, 
    0.2065, 0.6187), X78_only = c(0.3379, 0.4102, 0.2134, 0.6807, 
    0.8242, 1, 0.0046, 0.279), X8_removed = c(0.0967, 0.5831, 
    0.058, 0.9268, 0.3518, 0.0629, 0, 0.6229), X8_only = c(0.1169, 
    0.8327, 0.2169, 0.0907, 1, 1, 0.07, 0.486), X7_removed = c(0.2989, 
    0.7268, 0.0087, 0.8874, 0.5853, 0.0568, 0, 0.7622), X7_only = c(1, 
    0.5714, 0.2825, 0.8673, 0.5557, 0.6861, 0.0044, 0.1146), 
    X5_removed = c(1, 0.1453, 0.0176, 0.8428, 0.2277, 0.2563, 
    0, 0.5326), X5_only = c(0.0642, 0.631, 0.5193, 0.979, 0.5348, 
    0.1304, 0.02, 0.0217), X4_removed = c(0.4492, 0.3821, 0.0121, 
    0.9957, 0.5158, 0.0498, 0, 0.718), X4_only = c(0.6485, 0.0709, 
    0.1639, 0.6908, 1, 1, 0.4469, 0.639), X3_removed = c(0.3009, 
    0.3414, 0.02, 0.9935, 0.4216, 0.1273, 0, 0.6406), X3_only = c(1, 
    0.9325, 0.772, 0.5505, 1, 0.2068, 0.0829, 0.17), X2_removed = c(0.6335, 
    0.349, 0.2095, 0.9777, 0.8928, 0.0571, 0, 0.4285), X2_only = c(0.191, 
    0.4397, 0.0403, 0.3606, 0.0089, 1, 0.0033, 0.659), X1_removed = c(0.1653, 
    0.7658, 0.0718, 0.7705, 0.4193, 0.1894, 0, 0.5167)), .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 = c(NA, 8L), class = "data.frame")

split1_datam<-melt(split1_data,id="Loci")

p1<- ggplot(split1_datam, aes(x =Loci, y = value, color = variable, width=.15)) +  
         scale_fill_grey() + 
         geom_bar(position="dodge")+ 
         geom_hline(yintercept=0.05)+ 
         opts(axis.text.x  = theme_text(angle=90, size=8)) +
         scale_y_discrete(breaks=seq(0,1)) + 
         ylab(NULL)
p1

However, I was hoping to make the plot greyscale, but can’t seem to figure out how to accomplish this (note: the scale_fit_grey() depicted above is not working for me). Any suggestions? Thanks so much!

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1 Answer

  1. Editorial Team

    One thing that commonly trips people up at the start with ggplot2 is the difference between color and fill. For 2D objects like bars, rectangles, basically any filled area, color affects the border color and fill affects the interior color.

    In your plot, you map color = variable, but there is no mapping for fill in aes. I wonder if you meant fill = variable inside aes() and then to use scale_fill_grey.

    Otherwise, you’d use color = variable and scale_color_grey, but that would only “color” the borders of the bars, not the filled areas.

    For instance, with fill = variable and scale_fill_grey() I get something like this:

    enter image description here

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