Error in ggplot

Question

I am trying to make a ggplot. When I had shape in aesthetics, the code was working just fine. However, I need to put shape in geom_point() because I'm trying to reproduce a figure. And when I added shape to geom_point() it gave me the following error:

Aesthetics must be either length 1 or the same as the data (6): shape

I've looked for other answers here but apparently, nothing seems to be working for me. Above I've provided with an image of what my data looks like. There are 17000 entries.

Below is my code:

summarised_data <-ddply(mammals,c('mammals$chr','mammals$Species','mammals$chrMark'), 
function (x) c(median_rpkm = median(x$RPKM), median = median(x$dNdS)))

ggplot(summarised_data,aes(x = summarised_data$median_rpkm, y = summarised_data$median, 
color = summarised_data$`mammals$Species`)) + geom_smooth(se = FALSE, method = "lm") +
geom_point(shape = summarised_data$`mammals$chrMark`) + xlab("median RPKM") + ylab("dNdS")

  "ENSG00000213221", "ENSG00000213341", "ENSG00000213380", "ENSG00000213424", 
   "ENSG00000213533", "ENSG00000213551", "ENSG00000213619", "ENSG00000213626", 
  "ENSG00000213699", "ENSG00000213782", "ENSG00000213949", "ENSG00000214013", 
   "ENSG00000214338", "ENSG00000214357", "ENSG00000214367", "ENSG00000214517", 
    "ENSG00000214814", "ENSG00000215203", "ENSG00000215305",      "ENSG00000215367", 
   "ENSG00000215440", "ENSG00000215897", "ENSG00000221947", "ENSG00000222011", 
   "ENSG00000224051", "ENSG00000225830", "ENSG00000225921", "ENSG00000239305", 
   "ENSG00000239474", "ENSG00000239900", "ENSG00000241058", "ENSG00000242247", 
   "ENSG00000242612", "ENSG00000243646", "ENSG00000244038", "ENSG00000244045"), 
  class = "factor"), Species = structure(c(1L, 1L, 1L, 1L, 1L, 
   1L, 1L, 1L, 1L, 1L), .Label = c("Chimp", "Gori", "Human", "Maca", 
    "Mouse", "Oran"), class = "factor"), labs = structure(c(2L, 2L, 
    2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L), .Label = c("Chimp-A", "Chimp-X", 
    "Gori-A", "Gori-X", "Human-A", "Human-X", "Maca-A", "Maca-X", 
    "Mouse-A", "Mouse-X", "Oran-A", "Oran-X"), class = "factor"), 
     chrMark = structure(c(2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 
      2L), .Label = c("A", "X"), class = "factor"), chr = structure(c(27L, 
      27L, 27L, 27L, 27L, 27L, 27L, 27L, 27L, 27L), .Label = c("1", 
      "10", "11", "12", "13", "14", "15", "16", "17", "18", "19", 
      "2", "20", "21", "22", "2a", "2A", "2b", "2B", "3", "4", 
        "5", "6", "7", "8", "9", "X"), class = "factor"), dN = c(3.00669, 
       3.27182, 7.02044, 1.01784, 3.0363, 2.32786, 4.92959, 3.03753, 
       3.0776, 1.02147), dS = c(3.15631, 5.87147, 3.13716, 2.05438, 
       4.10205, 5.24764, 4.2014, 3.18086, 5.4942, 3.02169), dNdS = c(0.9525965447, 
     0.5572403504, 2.2378329444, 0.4954487485, 0.7401908802, 0.4436013141, 
1.1733207978, 0.954939859, 0.5601543446, 0.3380459279), RPKM = c(31.6, 
13.9, 26.3, 9.02, 11.3, 137, 242, 1.05, 59.4, 10.1), Tau = c(0.7113820598, 
0.8391023102, 0.3185943152, 0.6887167806, 0.9120531859, 0.6254200542, 
0.7165302682, 0.7257435312, 0.2586613298, 0.6493567251), 
GC3 = c(0.615502, 0.622543, 0.393064, 0.490141, 0.461592, 
0.626407, 0.490305, 0.482853, 0.346424, 0.466484)), .Names = c("gene", 
 "Species", "labs", "chrMark", "chr", "dN", "dS", "dNdS", "RPKM", 
  "Tau", "GC3"), row.names = c(NA, 10L), class = "data.frame")

Could you provide the data (mamals) you are using? Using dput for example. — Pop
– Pop, Commented Nov 25, 2016 at 14:51
I've added the image of my original dataset on which I use ddply — Lauren boomer
– Lauren boomer, Commented Nov 25, 2016 at 14:58
Use dput instead, something like dput(head(mydf, 20)) then copy the results into your question as a codeblock. — lmo
– lmo, Commented Nov 25, 2016 at 14:59
Looks like you miscopied, the result of dput should start with structure(... — Brandon Bertelsen
– Brandon Bertelsen, Commented Nov 25, 2016 at 15:12

Scott Warchal · Accepted Answer · 2016-11-25 19:02:41Z

1

There's a few things wrong with your code and how ggplot handles non-standard evaluation, I'd recommend reading a ggplot tutorial or the docs. Having a column called within summarised_data called 'mammals$species' and 'mammals$chrMark' is going to cause lots of problems.

If we change these to something more sensible...

names(summarised_data)[names(summarised_data) == "mammals$species"] <- "mammals_species"
names(summarised_data)[names(summarised_data) == "mammals$chrMark"] <- "mammals_chrMark"

We can make the ggplot code more friendly. Note that shape has to been within aes, as you're mapping it to your data.

ggplot(summarised_data, aes(x = median_rpkm, y = median)) + 
    geom_smooth(se = FALSE, method = "lm") +
    geom_point(aes(shape = mammals_chrMark,
                   color = mammals_species)) +
    xlab("median RPKM") + ylab("dNdS")

Hopefully this should work, or at least get you somewhere closer to an answer.

answered Nov 25, 2016 at 19:02

Scott Warchal

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1 Comment

Lauren boomer Over a year ago

Yes, it worked. Thankyou so much :) I've been banging my head against it for whole day.

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