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hputnam / Moorea_Sym

Symbiodinium communities of specifist and generalist corals
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finalize figures #25

Closed jrcunning closed 6 years ago

jrcunning commented 7 years ago

img_6586 jpg

jrcunning commented 7 years ago

make horizontal clade barplot figure 2

jrcunning commented 7 years ago

find new colors for clades

jrcunning commented 7 years ago

Created Figs 1 through 4 with d8c9da0

hputnam commented 7 years ago

replot Figure 1 with A,B,C visible Figure 1A with map Figure 1B with larger x and y lims Figure 1B and 1C with clearer biplot ids Figure 2 with dark brown for clade A? (gray too similar to light purple?) Figure 3 with error bars in front of symbols Figure 4 add temp metrics on X axis

daniclaar commented 7 years ago

Fig 3 Panel C, move purple sites on top of green sites? (to show no difference in location but that there is a difference in dispersion)

daniclaar commented 7 years ago

Worked on figure 1, but I am having issues with adding the moorea map to the current plot at a high enough resolution. I tried several different approaches, and none are working right now. Will try again later.

I put the error bar symbols in front for Figure 3, and did a bit of formatting. After messing around with it, I think that it is actually better that the purple sites are under the green sites on this figure, so I did not change the order.

I also changed all image output from the data_analysis.Rmd to TIFF, for ms submission later on.

daniclaar commented 7 years ago

I tried again to get the Moorea map into Figure 1. I have used the exact same code that I used on all of my other figures with images (and it has worked fine there!) I am at a bit of a loss about what to do here. I don't really have any other ideas to try that I haven't tried already, except 1) Just putting them together in photoshop (but will not self-make in the Makefile), or 2) Getting a shapefile for Moorea (maybe Hollie you have one, or the LTER may have one available?) and just going ahead and remaking the whole figure again. Sorry guys!

hputnam commented 6 years ago

@daniclaar can you knit again and see if Fig 1 is finalized?

daniclaar commented 6 years ago

Just knitted and pushed - I've fixed panel 1A to have larger text, made all three panels similar size, and changed the labels from column names to full words. Should be complete in commit 4443cf51a17469deded0083811cdc5e7825bcf85 but have a look and let me know what you think!