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TobiTekath / DTUrtle

Perform differential transcript usage (DTU) analysis of bulk or single-cell RNA-seq data. See documentation at:
https://tobitekath.github.io/DTUrtle
GNU General Public License v3.0
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Further help needed with transcript mapping fonts #18

Closed SianPiret closed 3 weeks ago

SianPiret commented 11 months ago

Hi - I'm still having a problem in which I get boxes instead of arrows when plotting the transcripts view, per issue #3. I'm on mac OS 12.6.2, R 4.2.2, DTUrtle 1.0.2

I used showtext to import Apple Symbol:

font_add(family = "Apple_Symbol", regular = "/System/Library/Fonts/Apple Symbols.ttf") showtext_auto() Then the lines you suggested in the earlier issue work perfectly: par(family = "Apple_Symbol") plot(1:5, t = "n") text(2,2,c(intToUtf8(c(11014))),cex=3) text(4,4,c(intToUtf8(c(11015))),cex=3) To produce: AppleSymbolTest

But still when I then try it for the transcript view plotting, I still get the boxes: plot_transcripts_view(dturtle = dturtle, genes = "HEY1", gtf = "../gencode.v34.annotation.gtf", genome = 'hg38', one_to_one = TRUE, arrow_colors = c("#7CAE00", "#D30000"), family="Apple_Symbol") Transcript_view_eg

Any further help appreciated!

Hi @lijinw ,

so we definitively found the culprit. To fix the issue, you must find a font supporting at least these two glyphs.

You could have a look at the extrafont or showtext packages - these shall allow you to import additional fonts.

Again, you might try the "Apple Symbols" font that should be pre-installed on your system. At least according to Wikipedia it should support the needed Glyphs (see here).

Originally posted by @TobiTekath in https://github.com/TobiTekath/DTUrtle/issues/3#issuecomment-984548209

m-noonan commented 10 months ago

Hi, related to this question, is there a way to increase the font size of the transcript name (ie HEY1-202)? I tried adding the 'pointsize' option in 'plot_transcripts_view' but it didn't seem to change the font size.

TobiTekath commented 5 months ago

@SianPiret Sorry, but as I do not have an Apple device, this problem is not easily debug-able for me. The font system under macOS seems to be a bit more complicated as I initially thought when deciding to include the arrows as UTF-8 symbols.

@m-noonan Please have a look at the thid value of the fontsize_vec. Increasing it to e.g. c(10, 1.1, 0.9) should increase the label font size.