SI figure document

[srcorsi-USGS]

Would a Rmarkdown document work to pull all of the SI figs into one place in the proper format? If so, @ldecicco-USGS could you pull this together? If not, let's discuss how it would be best to render this doc.

[srcorsi-USGS]

@ldecicco-USGS Here, I am keeping a list of the SI figures. If we need anything revised, there will be separate issues for individual SI figures.

1. SI-1 Site map (from OWC paper)
2. Detection level boxplot
3. Bar chart with number of sites with EAR>10^-3 per chemical.
4. Heat map with chemicals on Y-axis (color indicates priority chemical) and site on X-axis.
5. Figures A-M: Stacked bar charts by chemical class
6. Heat map with AOP ID on Y-axis and sites on X-axis
7. Mixtures boxplots

[ldecicco-USGS]

Current SI figure workflow:

# Fig SI 2:
source("SI2_detection_levels.R", print.eval=TRUE)
rm(list=ls())

# Fig SI 3:
source("SI3_chem_counts.R", print.eval=TRUE)
rm(list=ls())

# Fig SI 4:
source("SI4_heat_map.R", print.eval=TRUE)
rm(list=ls())

# Fig SI 5:
source("SI5_class_stacks.R", print.eval=TRUE)
rm(list=ls())

# Fig SI 6:
source("SI6_AOP_heat.R", print.eval=TRUE)
rm(list=ls())

@srcorsi-usgs do you have the "mixtures boxplots" script somewhere?

[srcorsi-USGS]

SI7_boxplots_mixtures.R

[ldecicco-USGS]

If you want me to do anything with that script, you'll need to add "SI_table7 Num_sites_by_mixture.csv" to the repo.

[srcorsi-USGS]

Sent a pull request: by running fig4_Data_summaries_for_manuscript.R, the file SI_table7 Num_sites_by_mixture_temp.csv is generated. That file is used to generate fig SI-7 mixtures boxplots. I can't test this to make sure it runs right now because I am getting an error in the data_setup.R script. @ldecicco-USGS

[srcorsi-USGS]

The SI figs should all be in one pdf including the map (SI-1) that I uploaded to the repo today (SI1 Map.pdf). The figure captions need to be included under each figure. I have added a file with the figure captions SIfigureCaptions.txt. Figure SI-5 already has captions built into them. Technically, they should be moved from the top of the figure to the bottom to fit journal style. Generating them individually and then piecing together later should work fine. I am not sure how to do it properly in R otherwise. @ldecicco-USGS

[ldecicco-USGS]

Getting those captions formatted right is a bit tricky...but I think I've figured out the trick now. Can you double check the text for SI fig 3? The others are on the way

[ldecicco-USGS]

Question on the heat map....do we want the full sub-scripted legend title like I copied above or leave it back as "max EAR". The spacing gets a bit trickier because it's a wider legend title. I can bump down the font size a bit and get Ontario back to not being cut off.

[srcorsi-USGS]

I have updated the fig titles and sent a PR. Here is one that I had in there for Fig 6 in another location:

Figure SI-6. Maximum exposure activity ratios (EARs) by site for individual Adverse Outcome Pathways (AOPs), summations within chemical classes, and summations for all chemicals measured in water samples at individual Great Lakes tributaries monitored from 2010-2013.

It doesn't match what we currently have, but did we have this kind of uber super comprehensive figure at some point or was this my pipe dream of the ideal summary of all results that never came to pass?

[ldecicco-USGS]

I think we decided that the 2 heat maps would be less confusing and cover the same ground.