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rggplot2graphicsgeom-bar

ggplot2 PDF barplot have white lines, require extensive zoom-ins and look diff. on PowerPoint

I am trying to plot a stacked bar plot in ggplot2 of multiple samples; however, when I graph my data, the PDF is riddled with white lines on each barplot.

Here is some example code so you can see what my data looks like:

Expt <- as.data.frame(round(replicate(10, runif(10, 0, 5)), 3))
colnames(Expt) <- c("S_3", "S_5", "S_12", "S_22", "S_25", "S_27", "S_33", "S_52", "S_100", "S_101")
Expt$Phyla <- c("Proteobacteria", "Firmicutes", "Actinobacteria", "Bacteroidetes", "Verrucomicrobia", "Planctomycetes", "Cyanobacteria", "Chlamydiae", "Chloroflexi", "Deinococcus")
colors <- c("navajowhite4", "dodgerblue", "cyan", "orange", "lawngreen", "burlywood1", "black", "pink", "slateblue2", "hotpink")

library(reshape2)
Expt_melt <- melt(Expt, id.vars = "Phyla")
colnames(Expt_melt)[2:3] <- c("Sample", "Abund")

library(ggplot2)
ggplot() + geom_bar(aes(x = Sample, y = Abund, fill =     Phyla), data = Expt_melt, stat = 'identity') + scale_fill_manual(values = colors)

This code produces a nice stacked barplot; however, my data has well over 6000 rows and many more samples and the actual image I get in return looks different dep. on the medium I use. Different Graphics

Any ideas as to why this is occurring? I need to be able to use the graph at PDF Zoomed at 150% when I insert it into a a normal powerpoint slide w/out it looking riddled with internal white lines. Not to mention, eventually, these graphs will get published and I cannot turn in a PDF that looks right when only zoomed in at 150%.

Looking into the the white line issue, I found this link to get rid of the internal bar lines: Getting Rid of Internal Bar Lines in a Bar Plot and following their code, I graphed my data using this code: 

ggplot(Expt_melt, aes(x= Sample, y=  Abund, fill = Phylum)) + stat_summary(fun.y = sum, geom = "bar") + scale_fill_manual(values = colors)

This produced the following graph:

stat_summary output

As you can see, this completely deleted all of my top bars - which were my Phyla (Expt_melt$Phyla) with lower Expt_melt$Abund values. Not to mention, this graph has to be zoomed in at 200% to be seen 'normal'.

Any suggestions on what to do? Any ideas as to why these graphs are exhibiting this behavior?

Thank you!

Solution

  • The default width of bars in ggplot is 0.9 (on a categorical axis where each level has a width of 1), so by default there are gaps between the bars. You may want to try setting width = 1:

    ggplot() + 
    geom_bar(aes(x = Sample, y = Abund, fill =     Phyla), 
             data = Expt_melt, stat = 'identity', 
             width = 1) + 
    scale_fill_manual(values = colors)