Improve/modify MSnbase sticker about biocstickers HOT 37 CLOSED

What about something like this - I have reduced peaks intensities and added a light transparency in the label and moved the peaks up a but. Haven't changed peaks colours yet.

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the ggtree sticker is reproducible in R.

I will make a pull request to add the source code.

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@lgatto now ggtree and treeio stickers are purely produced in R.

GIMP is not needed.

The tricky thing to remove background is using +ggtree::theme_transparent() + ggsave(bg='transparent').

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this plot itself is in hexagon shape 👏

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@jotsetung what about this?

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If time allows, I will have a go.

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For MSnbase, I thought maybe something like

(from ?MSmap)

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RFC - @jotsetung @sgibb @GuangchuangYu

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Two more things @lgatto @GuangchuangYu : for printing, the height of the image should ideally be 5cm. I would suggest that you create the pngs also in this size so they don't have to be resized later.

@lgatto have you tried to use white for the box edges? That could also look cool (eventually a little transparency too). I am also a little concerned with the width of the box lines, they look very thin and might make problems at the printing.

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sry, could have post it directly. The colour for the map: #96281b (and I used a slightly lighter background: #f9690e)

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It actually needs a transformation, not a rotation, to make it look perspectivly fitting (as seen below, its already perfectly parallel on the left). Not sure if that is possible within R.

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I think it looks great! (Except the font, I somehow don't fancy it.)
The plots for all the stickers are hand-drawn, as far as I can see. Is this meant to be the last version, or a draft?

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Yes, the font... I tried different ones (inconsolata etc) but didn't really like them either. Feel free to play with it in Gimp and change the font.
Regarding the graphs in the stickers, yes, for xcms and ensembldb it's the final version - I like the low-fi drawings ;)
For MSnbase it's just a proposal - didn't really know what to use as a graphic.

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I do like the low-fi drawings. But a reproducible figure produced in R, with the package would be cool too :-)

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I agree - do you plan to create such a plot?

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@jotsetung I have been thinking about the sticker and was wondering if the current MSnbase design wouldn't be a good fit for mzR, or do you have something else on stock?

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Yes, makes sense; then I'll do an mzR sticker with that. Do you have any ideas for a MSnbase design? Pbase could have something like the mapping plot from peptide features to genome, but MSnbase is not that easy I find.

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Awesome!

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I should probably lower the text a bit.

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I think you can rotate the figure a little bit.

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Rotation doesn't disturb me - actually, I think it might be too symmetric if you rotate it to have a 45 degree.
Did you create this in R?

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yes, eventually the text slightly lower - does it align with the others?

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Did you create this in R?

See MSnbase_sticker.R

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the text slightly lower

Done. @jotsetung - what about raising the text in xcms and mzR a bit?

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actually, it's the fault of ensembldb, I can't raise the text more there because otherwise the text doesn't fit anymore. That was the reason for the lower text I have (also in the template), to accommodate also for longer package names.

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May be we should check the average package name length and set the default based on that :-). My point is that ensembldb is an exception with the fancy leading e!.

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I checked the text position for the official stickers: the bottom text alignment for most stickers is 18mm from top. I'll adjust the template and the manually crafted stickers accordingly.

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Yes, I like that!

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@lgatto I would remove the border of the coordinate system completely (and change the gray/blue color of the map), e.g.:

Is it possibly to rotate the map a little bit? So that the m/z axis is parallel to the edge of the hex?

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@sgibb - I like that colour. Could you give me the specs. I will try to rotate a bit more, and see how it looks like.

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You could also leave the "box()" and align the plot to the sticker margins so that it takes over the entire area of the sticker.

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I am not sure I will manage to get the x and y coordinates completely parallel to the sticker margins. I think this would require to tilt in the z dimension, which doesn't looks as good. In the meantime, here's another iteration. (Updated since first post)

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I like that one - eventually you could move the plot a little bit up so that there is a smaller gap between the text and the plot - there's however this nasty signal in the right corner ;)

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The color you are using now is a little loud - could you eventually try to use #d35400?

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I think #d35400 is too close to the background and might not be visible once printed. I'll try something between #d35400 and #96281b later.

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Could you rotate it counter-clockwise a few degrees?

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The MSnbase sticker looks great. I'm closing the issue - @lgatto you can reopen if you're not yet done with the final design.

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