how to plot 3 data.frames in R ggplot2

Question

I have 3 data frames:

head(df1)

  Row.names       NMDS1       NMDS2 Station
1     E01M1 -1.39917737 -0.52996467     S01
2     E01M2 -0.85390268 -0.24919481     S01
3     E01M3 -0.31713304  0.14375418     S01
4     E01M4 -0.54494214 -0.12534209     S01
5     E02M1  0.03874897 -0.10945807     S02
6     E02M2  0.68255493 -0.07708227     S02

head(df2)

              NMDS1      NMDS2 env.pvals env.variables
Deep      0.23990125 -0.3194394 0.5384615          Deep
Salinity -0.18454375 -0.1849230 1.0000000      Salinity
Temp     -0.02935085  0.1953837 1.0000000          Temp
OD        0.27043891 -0.3425079 0.2967033            OD
pH        0.34483843 -0.1953211 0.6043956            pH
DBO5     -0.31011556  0.1377326 1.0000000          DBO5

head(df3)

               NMDS1      NMDS2 spp_pvals             Family
Otu_3503 -0.13102909  0.5044264     0.009 Desulfobacteraceae
Otu_3887 -0.09181908  0.5502878     0.004 Desulfobacteraceae
Otu_4287 -0.08140270  0.3914792     0.031 Desulfobacteraceae
Otu_4804 -0.10993229  0.5427913     0.005 Desulfobacteraceae
Otu_4807  0.21147428 -0.1891993     0.198   Desulfobulbaceae
Otu_5108 -0.45920996  0.0493874     0.012     Desulfatiglans

and I have tried to make a single plot from three df: df1, df2 and df3

plot df1

P <- ggplot(df1, aes(x = NMDS1, y = NMDS2)) + geom_point(aes(NMDS1, NMDS2, color = Station), size=4) + theme_bw()

plot df1 + df2

P <- P + geom_segment(data = df2, aes(x = 0, xend = NMDS1, y = 0, yend = NMDS2), arrow = arrow(length = unit(0.25, "cm")), colour = "grey10", lwd = 0.3) + 
    ggrepel::geom_text_repel(data = df2, aes(x = NMDS1, y = NMDS2, label = env.variables), cex = 4, direction = "both", segment.size = 0.25)

the problem!!!

I want to add the df3 plot to the previous P plot, using geom_point

ggplot(df3, aes(x = NMDS1, y = NMDS2)) + geom_point(aes(NMDS1, NMDS2, color = Family), size=2, shape=20, alpha=0.4) + theme_bw()

do I have to adjust scales ?, how could I plot all 3 df in a single plot ???

Thanks

Answer 1

Effectively your problem is that you need two color scales for two different sets of points.

There are solutions to this problem involving other packages such as ggnewscale , but an easier way to do it here is to use a shape that has a fill color for your larger points. shape = 21 would be ideal for your larger points. That way you can use the fill scale for Station and the color scale for Family . Just remember if you want to change the colors for the larger points you need to use scale_fill_xxx rather than scale_color_xxx

library(ggplot2)
library(ggrepel)

ggplot(df1, aes(x = NMDS1, y = NMDS2)) + 
  geom_point(aes(fill = Station), size = 5, shape = 21, color = "00000000") + 
  geom_segment(aes(x = 0, xend = NMDS1, y = 0, yend = NMDS2), data = df2,
               arrow = arrow(length = unit(0.25, "cm")), 
               colour = "grey10", lwd = 0.3) +
  geom_text_repel(aes(label = env.variables), data = df2,
                  cex = 4, direction = "both", segment.size = 0.25) +
  geom_point(aes(color = Family), data = df3, size = 2, shape = 20) +
  theme_bw()