ggplot2 not getting colors assigned in legend values

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I have generated the following code for a plot:

ggplot(Table_Final_v0, aes(x=log2(SeqCount_a+1), y=log2(SeqCount_m1+1), fill=kingdom2, color=Color_point2)) + 
  geom_point(size=Size_point, alpha=0.8, color=Color_point2) + scale_color_manual(values = Color_point2) +
  theme_classic() + ylab("log2(Sequence Count -m 1)\n") + xlab("\nlog2(Sequence Count -a)") + ylim(0,14) + xlim(7,17) + 
  geom_text(label=species, nudge_x = -0.5, nudge_y = 0.5, check_overlap = T, show.legend = F, color="black") +
  theme(axis.text.x = element_text(size=10), axis.title=element_text(size=12), 
        axis.text.y =element_text(size=10),plot.margin = margin(1, 0.5, 0.5, 1, "cm")) + ggtitle(title) +
  theme(plot.title = element_text(size = 14)) + theme(legend.title=element_blank())

Which generates the following plot:

enter image description here

And the Table_Final_v0 looks like this:

rRNA                 Seq_count_m1 Seq_count_a  Size_point    species      kingdom2    Color_point2
Loxodonta_africana            178       18722          6         Laf      Elephant          red3
Acyrthosiphon_pisum             0       50324          4         Api       Insects   dodgerblue3
Aedes_aegypti                   0       36776          4         Aae       Insects   dodgerblue3
Aegilops_tauschii              26       17539          4         Ata        Plants   forestgreen
      .                         .           .          .         .           .        .  
      .                         .           .          .         .           .        .

As you can see, the kingdom2 variable contains the names appearing in the legend, and the Color_point2 variable includes the colors I would like to display in the plot and also in the legend. But somehow I could not manage to assign them to the legend, and they only appear in the plot.

What is wrong with the code? I would like the colors to appear as well in each label in the legend like it should be doing with scale_color_manual

ggplot2 legend r colors
1 Answers

This could be one option to achieve your task.

ggplot(df, aes(x=log2(Seq_count_a+1), y=log2(Seq_count_m1+1), color=kingdom2)) + 
  geom_point(size=df$Size_point, alpha=0.8) +
  scale_fill_manual(values = df$Color_point2) +
  theme_classic() + 
  ylab("log2(Sequence Count -m 1)\n") + 
  xlab("\nlog2(Sequence Count -a)") + 
  ylim(0,14) + 
  xlim(7,17) + 
  geom_text(label=df$species, nudge_x = -0.5, nudge_y = 0.5, check_overlap = T, show.legend = F, color="black") +
  theme(axis.text.x = element_text(size=10), 
        axis.title.x = element_text(size=12), 
        axis.text.y = element_text(size=10), 
        plot.margin = margin(1, 0.5, 0.5, 1, "cm"),
        legend.title=element_blank()
        )

enter image description here

Data:


df <- tribble(
~rRNA,                 ~Seq_count_m1, ~Seq_count_a,  ~Size_point,    ~species,      ~kingdom2,    ~Color_point2,
"Loxodonta_africana",  178,   18722, 6,    "Laf",  "Elephant", "red3", 
"Acyrthosiphon_pisum", 0,     50324, 4,    "Api",  "Insects",  "dodgerblue3", 
"Aedes_aegypti",       0,     36776, 4,    "Aae",  "Insects",  "dodgerblue3", 
"Aegilops_tauschii",   26,    17539, 4,    "Ata",  "Plants",   "forestgreen")
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