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")

Answer 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.