zkamvar
commented
6 years ago Okay, so there are some easy things here and some technically challenging things:
Easy
Tables and Figures
- [x] rename figures as Fig1.pdf ... Fig6.pdf
- [x] tell PeerJ where they can find the tables
- [x] Figure 6 was fine in the review, I see no reason to change it now 😤
Removing stuff
- [x] remove funding statement from manuscript
- [x] use full names in funding statement (must be done on PeerJ site @sporangia)
- [x] remove competing interests info from manuscript
- [x] remove author contributions from manuscript
"Data not shown"
This is a joke, right? We have the data in this repository AND the statement refers to edges that aren't shown extending to nodes that exist outside of the context of the figure which are shown in the supplementary figure.
- [x] address concerns about Fig 1A
- [x] address concerns about Fig 1C
Hard
Separating supplementary materials
One of the reasons why this is hard is because the internal references (e.g. Fig. S1) are automatically generated, which means that we will need to post-process the tex document. I believe I can engineer something on the command line.
The answer to implementing this may be here: https://tex.stackexchange.com/a/157118/77699
- [x] Separate supplementary figures into individual files
Figures
1) Please upload your figures in either EPS, PNG, or PDF (vector PDFs only), measuring at least 900 by 900 pixels and eliminating excess white space around the images, as primary files here https://peerj.com/manuscripts/20972/files. 2) Please use numbers to name your files, example: Fig1.eps, Fig2.png. 3) Figure 6 has multiple parts. Each part needs to be labeled alphabetically to use (A, B, C and D). Please provide a replacement figure measuring at least 900 by 900 pixels, saved as PNG, EPS, or PDF (vector images) file format without excess white space around the images. Each figure with multiple parts should label each part alphabetically (e.g. A, B, C and D) and all parts of each single figure should be submitted together in one file. 4) If you have figures composed in the LaTeX source file we can use that at the time of production. Please leave a Note to Staff at https://peerj.com/manuscripts/20972/declarations/#other if you choose to provide the figures in the LaTex source file so that staff will know that's where it can be found. (example note to staff: Figure 1 and 2 are in the source file manuscript and can be found in the .tex file).
Tables
1) We ask for the tables in Word (composed in Word, not images pasted in Word docs), but if you have them composed in the LaTeX source file we can use that instead at the time of production. 2) Please leave a Note to Staff at https://peerj.com/manuscripts/20972/declarations/#other if you choose to provide the tables in the LaTex source file so that staff will know that's where it can be found. (example note to staff: Tables 1, 2, 3 are in the source file manuscript and can be found in the .tex file).
Remove Supplemental Files from Manuscript Source File
The supplemental files should only be supplied as separate files in the Supplemental Files section and should not appear in the manuscript source document. Please remove them from the manuscript document and re-upload the manuscript here: https://peerj.com/manuscripts/20972/files, and then upload the Supplemental Files separately in the appropriate section. Supplemental Files are not typeset, they are published as downloadable files with the titles and legends exactly as they are entered into the system, so please ensure the titles and legends are complete. Examples of such legends are here: https://peerj.com/articles/2344/#supplemental-information.
Data not Shown
We noted your statement “Data not Shown” (in the Figure 1 legend "Edges extending from MLHs displayed to other MCGs are not shown"). We would like to draw your attention to our Data Sharing policy as detailed at https://peerj.com/about/policies-and-procedures/#data-materials-sharing. Of course, the inclusion of this statement does not necessarily mean that our policy is being violated, so please can I ask you to leave a note to staff at https://peerj.com/manuscripts/20972/declarations/#other or email me (at editorial.support@peerj.com) to let me know the reason(s) for not showing this data in this instance?
Funding Statement
1) Please remove all financial and grant disclosure information from the source file manuscript. This information should only be provided in the Funding Statement here: https://peerj.com/manuscripts/20972/declarations/#question_18. 2) Please use full names, instead of initials, for the author names in the Funding Statement. Edit here https://peerj.com/manuscripts/20972/declarations/#question_18.
Competing Interests
Please remove all competing interests information from the source file manuscript and make sure it is included in your Competing Interest Statement instead here https://peerj.com/manuscripts/20972/declarations/#question_17.
Author Contributions
Please remove all author contributions information from the source file manuscript and make sure it is included in your Authorship Statement instead here https://peerj.com/manuscripts/20972/declarations/#authorship.