'dot Plot' relative to mean with standard deviation

Question

Good morning

In the attached graph, the points refer to the value of the average selectivity of each species. On this chart, I’d like to:

1) have larger font sizes of smaller body mass <9kg points. I wanted to reduce the scale of difference between the points by placing the smaller ones slightly larger, but keeping the other larger ones (body mass species > 9kg) in the same size. If not possible, I would like to at least increase the font size of the dots.

2) I would also like to add a black border around the dots (just to highlight the dots)

3) I would like to add the standard deviation (sd) of each midpoint. Mean and standard deviation values are shown respectively in the columns "media" and "sp".

Could someone help me? Thanks in advance :)

library(tidyverse)
Dataset %>%
ggplot(aes(x = media, y = specie, 
             colour = energetic_level, size = log(bodymass))) +
  geom_point(alpha = .9) +
  scale_colour_continuous(low = 'green', high = 'red') +
  labs(x = 'media', y = 'Species') +
  ggthemes::theme_few() +
  theme(axis.text.x = element_text(angle = 90, vjust = .5)) 

media   dp  specie  bodymass    energetic_level
4.063478961 3.627269468 AAChlor_cyn 5000.01 3.2
4.05537378  3.585436083 ABOtol_cras 1206.61 2.4
3.999309751 3.818689333 ACMiop_tal  1248.86 3
3.945049659 3.855743536 BACerc_mit  5041.29 2.5
3.862515658 3.687924328 BCThry_swin 4000    2.8
3.655056928 3.732785731 DAHys_afri  14936.02    2.8
3.56041853  3.478167947 DBLep_cap   1500    3
3.402431689 3.446995588 DCCivet_civ 12075.58    4.6
3.401743858 3.569716116 FGenet_gen  1756.17 6.1
3.39029097  3.414370313 GALept_serv 11999.96    7
3.39009097  1.552336764 GBPhil_mont 4896.05 2.6
3.32029097  1.920646552 HOryct_afer 56175.2 5
3.239734182 3.540636613 IHipp_amph  1536310.4   3
3.154474564 3.526089786 JBSylv_grim 15639.15    3.2
2.883544415 3.007873613 MAPota_larv 69063.79    3.3
2.719993477 1.308813082 MBTrag_scri 43250.39    3
2.718552867 3.080761281 MCPant_pa   52399.99    7
1.982822501 2.085016316 MDRed_aru   58059.24    3
1.529854402 1.814623348 MFSync_caf  592665.98   3
1.443776834 1.254052861 NLox_afric  3824539.93  3
1.402107786 1.637998721 OCan_mes    22000   5.2
1.164299734 1.397597868 PPant_le    158623.93   6.8
0.887732043 1.318886523 QLyc_pict   21999.99    7
0.82952687  0.789227213 UCroc_croc  63369.98    7
0.782973623 0.570878282 VTrag_oryx  562592.69   2.7
0.477482615 0.624782141 YHipp_eq    264173.96   3

Answer 1

I believe the code below satisfies all that has been requested:

Dataset %>%
ggplot(aes(x = media, y = specie)) +
  geom_point(aes(fill=energetic_level, size=log(bodymass)), alpha = .9, 
    pch=21, colour="black", stroke=2) +
  scale_fill_continuous(low = 'green', high = 'red') +
  labs(x = 'media', y = 'Species') +
  ggthemes::theme_few() +
  theme(axis.text.x = element_text(angle = 90, vjust = .5)) +
  scale_size_continuous(range = c(3, 6)) +
  geom_errorbarh(aes(xmin=media-dp, xmax=media+dp), colour="black", size=.2) 

Now, let’s see how each item was obtained:

1) have larger font sizes of smaller body mass <9kg points. I wanted to reduce the scale of difference between the points by placing the smaller ones slightly larger, but keeping the other larger ones (body mass species > 9kg) in the same size. If not possible, I would like to at least increase the font size of the dots.

I solved this with the function scale_size_continuous(range = c(3, 6)). In it I determined that the smallest size for the points is 3 and, the largest, 6. Thus, the smallest point will have at least half the area of the largest. If the ratio did not please you, just change these numbers to arrive at a more aesthetically pleasing result. Note that the function scale_size_continuous(range = c(3, 6)) maintains the logarithm transformation applied to bodymass.

2) I would also like to add a black border around the dots (just to highlight the dots)

Suffice it to say that the symbol to be plotted is the pch=21. To the R, this means a round point with edge. With colour I define the color of the border and with stroke its thickness. I put a greater thickness to make it clear that it exists.

3) I would like to add the standard deviation (sd) of each midpoint. Mean and standard deviation values are shown respectively in the columns "media" and "sp".

Do this using the function geom_errorbarh(aes(xmin=media-dp, xmax=media+dp), size=.2). The limits of the error bar were defined as mean - standard deviation and mean + standard deviation. The color and thickness of the lines are defined with the arguments colour and size, respectively.