sdtaylor/complex_figure_examples

Gallery and R code for published scientific figures

complex_figure_examples's Issues

Lessons learned from making plots

Various things I'm noticing. Maybe worth a blog post or something.

Things which are hard and should be avoided:

1. Several very different plots in a single figure.

2. Custom axis text labels. eg in cottrell 2020.

Steel 2021

Steel, Z. L., Goodwin, M. J., Meyer, M. D., Fricker, G. A., Zald, H. S. J., Hurteau, M. D., & North, M. P. (2021). Do forest fuel reduction treatments confer resistance to beetle infestation and drought mortality?. Ecosphere, 12(1), https://doi.org/10.1002/ecs2.3344

Figure 6

pretty complex image, though each panel by itself is straightforward. Will have to describe 2+ dataframes needed.
The legend is very complex as it mixes them from the 3 panels. Potentially the newest patchwork releases can do this.

Lindberg et al. 2020 figure 2

Lindberg, C. L., Hanslin, H. M., Schubert, M., Marcussen, T., Trevaskis, B., Preston, J. C., & Fjellheim, S. 2020. Increased above ground resource allocation is a likely precursor for independent evolutionary origins of annuality in the Pooideae grass subfamily. New Phytologist. https://doi.org/10.1111/nph.16666

MacDougall 2020

MacDougall, Andrew H., et al. "Is there warming in the pipeline? A multi-model analysis of the zero emission commitment from CO2." Biogeosciences Discussions (2020): 1-45. https://doi.org/10.5194/bg-17-2987-2020

Very clever double bar graph

Engemann et al 2020

Engemann et al. 2020. Associations between growing up in natural environments and subsequent psychiatric disorders in Denmark. Environmental Research. https://doi.org/10.1016/j.envres.2020.109788.

figure 1, but only the right part

example of differentiating group and color in aes()

Daskalova et al 2020

Daskalova, G. N., Myers-Smith, I. H., Bjorkman, A. D., Supp, S. R., Blowes, S. A., Magurran, A., & Dornelas, M. (2020). Landscape-scale forest loss as a catalyst of population and biodiversity change. Science. https://doi.org/10.1126/science.aba1289

Also a preprint https://www.biorxiv.org/content/10.1101/473645v4.full

Figure 4, (fig 3 in preprint)

Dannenberg et al. 2020 cool bicolor map

Dannenberg, M., Wang, X., Yan, D., & Smith, W. (2020). Phenological Characteristics of Global Ecosystems Based on Optical, Fluorescence, and Microwave Remote Sensing. Remote Sensing, 12(4), 671. https://doi.org/10.3390/rs12040671

Klingbeil et al. 2021

Klingbeil, B.T., Cohen, J.B., Correll, M.D. et al. High uncertainty over the future of tidal marsh birds under current sea-level rise projections. Biodivers Conserv (2021). https://doi.org/10.1007/s10531-020-02098-z

Figure 2

Craven et al 2019 figure 5

Craven, D., Knight, T.M., Barton, K.E., Bialic-Murphy, L. and Chase, J.M., 2019. Dissecting macroecological and macroevolutionary patterns of forest biodiversity across the Hawaiian archipelago. Proceedings of the National Academy of Sciences, 116(33), pp.16436-16441. https://doi.org/10.1073/pnas.1901954116

Good example using position_dodge() with geom_point()
Fading effect showing the density of points is nice. Also good example showing how simple special characters are in the yaxis.

include watermark on bottom

Link to this repo

"This figure is a replication for educational purposes"
"The data may not match the original
"see https://github.com/sdtaylor/complex_figure_examples"

maybe a giant watermark of:
"Example figure. Not made with real data. For educational purposes only."
"see https://github.com/sdtaylor/complex_figure_examples"

Janssen et al. 2020

Janssen, T., Fleischer, K., Luyssaert, S., Naudts, K. and Dolman, H., 2020. Drought resistance increases from the individual to the ecosystem level in highly diverse neotropical rain forest: a meta-analysis of leaf, tree and ecosystem responses to drought. Biogeosciences. https://doi.org/10.5194/bg-17-2621-2020

Figure 1 is really nice

• 2 axis timeseries on the middle plot
• interesting shading on the bottom plot. probably done with a large amount of points instead of a single line.

Yin et al. 2020

Yin, X., Niu, Y., van der Putten, P. E., & Struik, P. C. 2020. The Kok effect revisited. New Phytologist. https://doi.org/10.1111/nph.16638

Figure 4

• using symbols and text instead of different colors to differentiate treatments

other resources

Relevant tutorials and things to link to

https://rpkgs.datanovia.com/ggpubr/ - package with shortcut functions for a lot of common figures

Nerlekar 2020

Nerlekar, A.N. and Veldman, J.W., 2020. High plant diversity and slow assembly of old-growth grasslands. Proceedings of the National Academy of Sciences, 117(31), pp.18550-18556. https://doi.org/10.1073/pnas.1922266117

Figure 1

create some classic plots

dont necessarily need to find published ones for these

• regression with equation/stats added using ggpmisc
• bar plot with anova sig. stars
• precip/temp plot with 2 y-axis

Zhang et al. 2020

Zhang, Qiang, et al. "Trait–environment relationships differ between mixed‐species flocking and non‐flocking bird assemblages." 2020. Ecology. https://doi.org/10.1002/ecy.3124

Ober et al. 2020

Ober, H.K., Jones, G.M., Gottlieb, I.G., Johnson, S.A., Smith, L., Brosi, B. and Fletcher, R.J., Jr. (2020), Bat community response to intensification of biomass production for bioenergy across the southeastern USA. Ecol Appl. Accepted Author Manuscript. doi:10.1002/eap.2155

This one is very straightforward and mostly a theme example

Haase et al. 2020

Haase, Catherine G., et al. 2020. "Body mass and hibernation microclimate may predict bat susceptibility to white‐nose syndrome." Ecology and Evolution. https://doi.org/10.1002/ece3.7070

Figure 2

Schwarz et al. 2020 Figure 1

Schwarz, B., Vázquez, D.P., CaraDonna, P.J., Knight, T.M., Benadi, G., Dormann, C.F., Gauzens, B., Motivans, E., Resasco, J., Blüthgen, N. and Burkle, L.A., 2020. Temporal scale‐dependence of plant–pollinator networks. Oikos. https://doi.org/10.1111/oik.07303

Thein et al. 2020

Thein, M. M., Wu, L. M., Corlett, R. T., Quan, R. C., & Wang, B. (2020). Changes in seed predation along a 2300‐m elevational gradient on a tropical mountain in Myanmar: a standardized test with 32 non‐native plant species. Ecography. https://doi.org/10.1111/ecog.05385

Figure 1

make readme a gallery

Can be done by just shoving all the images together. Links can point to respective pages.

No good way to have text by them like this though. Maybe a hover?

<img src="https://raw.githubusercontent.com/sdtaylor/complex_figure_examples/master/suggitt2019/suggitt2019_final.png" width="30%"> 
 <img src="https://raw.githubusercontent.com/sdtaylor/complex_figure_examples/master/yan2019/yan2019_final.png" width="30%"> 

Cottrell et al. 2020 fig 1

Cottrell, R.S., Blanchard, J.L., Halpern, B.S. et al. Global adoption of novel aquaculture feeds could substantially reduce forage fish demand by 2030. Nature Food 1, 301–308 (2020). https://doi.org/10.1038/s43016-020-0078-x

something with a map

Making some really nice maps w/ insets:
https://www.r-spatial.org/r/2018/10/25/ggplot2-sf.html
https://www.r-spatial.org/r/2018/10/25/ggplot2-sf-3.html

Fig 2 Deagle et al 2018

Deagle, BE, Thomas, AC, McInnes, JC, et al. Counting with DNA in metabarcoding studies: How should we convert sequence reads to dietary data?. Mol Ecol. 2019; 28: 391– 406. https://doi.org/10.1111/mec.14734

Interesting things:

• top and bottom x axis labels in the bar plots
• the "true" columns in the barplots. they probably need to be 3 figures gridded together
• placement of the large brackets
• x-axis spacing of the boxplots

Cook et al. 2020

Cook, B. I., Mankin, J. S., Marvel, K., Williams, A. P., Smerdon, J. E., & Anchukaitis, K. J. (2020). Twenty‐first century drought projections in the CMIP6 forcing scenarios. Earth's Future, 8(6), https://doi.org/10.1029/2019EF001461.

Miazgowicz et al. 2020

Miazgowicz K. L., Shocket M. S., Ryan S. J., Villena O. C., Hall R. J., Owen J., Adanlawo T., Balaji K., Johnson L. R., Mordecai E. A. and Murdock C. C. 2020. Age influences the thermal suitability of Plasmodium falciparum transmission in the Asian malaria vector Anopheles stephensi Proc. R. Soc. B. https://doi.org/10.1098/rspb.2020.1093

figure 2

Great example of plotting the curve of custom functions around observed data.

Guyton et al. 2020 - bar graph with animal silhouettes

Guyton, J.A., Pansu, J., Hutchinson, M.C. et al. Trophic rewilding revives biotic resistance to shrub invasion. Nat Ecol Evol 4, 712–724 (2020). https://doi.org/10.1038/s41559-019-1068-y

Figure 3

Reyes & Elias 2019 fig 5

Reyes, J. J., & Elias, E. (2019). Spatio-temporal variation of crop loss in the United States from 2001 to 2016. Environmental Research Letters, 14(7), 074017. https://doi.org/10.1088/1748-9326/ab1ac9

cool plot showing various sig. factors across a range of categorical locations and times.

Martinson et al. 2020

Not an article but a plot post. Super sweet figure though.

Tim Martinson, Al Kovaleski, and Bruce Reisch. 2020. Grape mapping populations reveal genetic variation in bloom and fruit development. https://www.vitisgen2.org/2020/07/09/reisch-mapping-populations/

Sullivan et al. 2020 figure 1

Sullivan et al. 2020. Long-term thermal sensitivity of Earth’s tropical forests. Science. 368:6493, 869-874. https://doi.org/10.1126/science.aaw7578

nice map that is not square. sizing needs to be fine tuned during saving

outline for readme within individual folders

Paper

Notes, interesting aspects

Original Figure (note license where applicable)

reproduced figure