ggplot2: using geom_point() and not all of my character labels are plotting on the X-axis

Question

I am trying to graph using the ggplot2 geom_point call in R. However, when I plot the desired graph, my X-labels that are words (not numbers) do not all show up on the X-axis.

To begin, here is some reproducible data:

Bac <- data.frame(logFC = seq(-1, 3.5, 0.19), 
             ASV_Fam = c("ASV_31; Bdellovibrionaceae", "ASV_152; Reyranellaceae", "ASV_102; Hymenobacteraceae", "ASV_124; Nitrospiraceae", "ASV_141; NA", 
                                                          "ASV_180; Microscillaceae", "ASV_259; Microscillaceae", "ASV_272; Chitinophagaceae", "ASV_79; Chthoniobacteraceae", 
                                                          "ASV_266; Chthoniobacteraceae", "ASV_106; Nitrosomonadaceae", "ASV_121; Nitrospiraceae", "ASV_184; Methylophilaceae", "ASV_115; Chthoniobacteraceae",
                                                          "ASV_123; Nitrosomonadaceae", "ASV_143; Haliangiaceae", "ASV_139; NA", "ASV_159; Micrococcaceae", "ASV_185; Xanthobacteraceae", "ASV_227; Chitinophagaceae",   
                                                          "ASV_233; NA", "ASV_239; Chitinophagaceae", "ASV_255; NA", "ASV_204; Longimicrobiaceae"), 
             Phylum = c("Bdellovibrionota", "Proteobacteria", "Bacteroidota", "Nitrospirota",     
                        "Proteobacteria", "Bacteroidota", "Bacteroidota", "Bacteroidota",     
                        "Verrucomicrobiota", "Verrucomicrobiota", "Proteobacteria", "Nitrospirota",     
                        "Proteobacteria", "Verrucomicrobiota", "Proteobacteria", "Myxococcota",      
                        "Proteobacteria", "Actinobacteriota", "Proteobacteria", "Bacteroidota",     
                        "Proteobacteria", "Bacteroidota", "Cyanobacteria","Gemmatimonadota"))

Bac$Family <- gsub("^[^.]*;", "", Bac$ASV_Fam)

The closest I have found to my error is this post: Unable to plot points from a data.frame. Following instructions from there, I added a factor with a single level by following the suggested code:

Bac$logFC <- factor(Bac$logFC, levels = unique(Bac$logFC))
Bac$ASV_Fam <- factor(Bac$ASV_Fam, levels = unique(Bac$ASV_Fam))

Graphing:

ggplot(Bac, aes(x = Family, y = logFC, color = Phylum)) + geom_point() +
scale_x_discrete(labels = toShow$ASV_Fam) + theme(axis.text.x = element_text(colour = "black", size = 9, angle = -90))

However, this still does not plot all of my X-labels that I need to see. Here is the graph I get:

As you can see, it only plotted 14 of my 24 labels I have passed for the X-axis. All of my points are there, but some vertical lines show more than 1 point and only 1 label is associated with that vertical line. See for example X-axis labels: ASV_152; Reyranellaceae, ASV_102; Hymenobacteraceae, ASV_266; Chthoniobacteraceae, etc.

I am not sure why these are not given separate X-axis labels and are instead being graphed on the same vertical line, thus reducing the total labels plotted on the X-axis.

Other work arounds I have tried: widening the pdf via the pdf() command, widening the graph by passing coord_fixed(ratio = 0.25), but none of these options work.

In addition, passing the following code scale_y_discrete(breaks = seq(-1, 4, 0.5)) so that I can not have so many numbers show up in the Y-axis does not work. I think it's because the y-axis has been set as a factor, so I tried to keep it numeric, but that isn't working either.

Any clue into what is going on would be very helpful!

For reference, here is the ouput of my session sessionInfo()

R version 4.1.1 (2021-08-10)
Platform: x86_64-apple-darwin17.0 (64-bit)
Running under: macOS Big Sur 11.6

score 1 · Accepted Answer · answered Oct 20 '21 at 02:53

1

When you check dim(table(Bac$Family)), there exists 14 unique values in Family, and as you set x axis of your plot by x = Family, there only 14 values exists.

I'm not sure about your purpose, but if you want all 24 labels(ASV_Fam) in x axis and one point per each, instead of x = Family, try x = ASV_Fam

Please let me know if this plot is not what you wanted.

ggplot(Bac, aes(x = ASV_Fam, y = logFC, color = Phylum)) + geom_point() +
  theme(axis.text.x = element_text(colour = "black", size = 9, angle = -90))

answered Oct 20 '21 at 02:53

Park

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Yes! This absolutely worked. Something so simple. Thank-you. However, the `scale_y_discrete(breaks = seq(-1, 4, 0.5))` added to the graph is still is not working. Any clues as to what is going on there? – Purrsia Oct 20 '21 at 03:02
1

I just answered my own question. I switched out `scale_y_discrete(breaks = seq(-1, 4, 0.5))` to `scale_y_continuous(breaks = seq(-1, 4, 0.5))` and the scaling works as intended. Thanks for your help! – Purrsia Oct 20 '21 at 03:46

ggplot2: using geom_point() and not all of my character labels are plotting on the X-axis

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