Figure: MMSEQ

Incorporate the MMSEQ figure (slide 6) in the slide-deck as part of the R-markdown workflow!

2019_GDB_udpate_2020_05_15__p6

Script: mmseq_upset_plot_w_metaspades.R

added Figure label

changed milestone to %Manuscript - initial version

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changed the description

@susheel.busi, @cedric.laczny

How about using UpSetR for this figure? It is great for displaying intersections. See the attached PDF for the first version. If needed I can highlight specific intersections.

mmseq_upsetr.pdf

Edit: Will need to remove Set Size I guess, because it is the sum of the intersections...

@valentina.galata Sure, can you please also add colours for the different assemblers, akin to the figure on the slide? Thx!

I can color specific intersections or complete rows (example 5). But, I cannot color each tool (i.e. dot in the row) separately. What kind of information do you want to encode/highlight by the color?

• not necessarily information, but colouring the different assemblers' bars more for ease of looking at a plot
• if there's no way to colour the bars, then I guess we live without it
• all grey just makes for a boring look ;)

• set size is not critical and can be inferred from the bottom left bars, or can be put in the text.. so, go for it!

And, thank you!!

You can color the bars, right? Not the dots :)

UPDATE: Strange, thought this was possible for the bars of the rows

UPDATE2: -> http://research.libd.org/rstatsclub/2018/07/27/hacking-our-way-through-upsetr/?utm_source=feedburner&utm_medium=feed&utm_campaign=Feed%3A+LIBDrstats+%28LIBD+rstats+club+--+rstats%29

I definitely do not want to "hack my way through" except I have one week time to work on this stuff only. ;) I already know this post and, as far as I can see, there was no merge request for that.

Fair enough :)

Here is another version with colors for each tool. mmseq_upsetr.pdf

That looks good to me.

I concur!

mentioned in commit b6c8e53e

Before using R-markdown, I will write scripts for each figure and save the plots as PDFs. That is easier and faster to implement; I will add R-markdown later.

closed

mentioned in commit a1a48734

mentioned in commit d789ece4

mentioned in commit d70ee8ea

changed title from figure-request-2: MMSEQ to Figure: MMSEQ