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Sage-Bionetworks / NF_LandscapePaper_2019

This repository hosts all the code used to generate analyses and figures for the landscape paper
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Figs #81

Closed jaybee84 closed 4 years ago

jaybee84 commented 4 years ago

Adding Fig2 and updated Fig3

allaway commented 4 years ago

Fig2B : can you change the colors to match the tumor type color scheme? Also, can you remove the ` from the LVs in the ridgeplots? here's a snippet to do that: mutate(lv_fix = stringr::str_replace_all(LV_Full," ",""))` (I just had this handy from doing the same this morning :) )

Figure 2: Looks good, can you make the abstract section a bit denser? Can you add something to clarify that you are testing on an independent set that was not used for feature selection in (iv/v)?

Figure 3: same comments as 2B.

This is a really hard comment to format with all the backticks but hopefully it's easy enough to copy and paste...haha

sgosline commented 4 years ago

I agree with Robert's suggestions.

jaybee84 commented 4 years ago

merging this closes #63

jaybee84 commented 4 years ago

Fig2B : can you change the colors to match the tumor type color scheme? Also, can you remove the ` from the LVs in the ridgeplots? here's a snippet to do that: mutate(lv_fix = stringr::str_replace_all(LV_Full," `","")) (I just had this handy from doing the same this morning :) ) Figure 2: Looks good, can you make the abstract section a bit denser? Can you add something to clarify that you are testing on an independent set that was not used for feature selection in (iv/v)? Figure 3: same comments as 2B.

This is a really hard comment to format with all the backticks but hopefully it's easy enough to copy and paste...haha

Thanks a bunch for the snippet! made life so much easier for me! :)