A problem when using netVisual_aggregate about cellchat HOT 13 OPEN

Hi,
This error generally occurs when non-standard fonts like Arial or Times New Roman are not available in your R session. (This has been mentioned before #29 (comment))
I was able to fix this as follows (Ubuntu):

1. Download TTF files for font Arial and Times New Roman, e.g. from here.
2. Unzip the files and put them into a reasonable directory, e.g. /home/USERNAME/fonts.
3. Install the R extrafont package, and add the following code to the header of your script:

library(extrafont)
font_import(paths="/home/USERNAME/fonts", prompt=F)
loadfonts(device = "pdf", quiet = F)

4. Run the code to generate PDF figures, for example:

pdf("/home/USERNAME/CellChat_results/network.pdf", width=7, height=7)
netVisual_aggregate(cellchat, signaling = pathways.show,  vertex.receiver = vertex.receiver, vertex.size = groupSize)
dev.off()

Worked like a charm for me.
Cheers.

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@chuiqin Try install.packages("extrafont")

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Thank you very much for your help!

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@chuiqin Try install.packages("extrafont")
I'm sorry but I still get the same error after installing packages("extrafont").

Error in text.default(x, y, labels = labels, col = label.color, family = label.family, : invalid font type

Can you help me with this problem again? Thank you!

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@chuiqin It looks like your R does not support 'Arial' font style when doing plotting. Can you google such issue based on your system of the computer as I did not hear of such issue from other users? The extrafont package is available here. In addition, please try save the plot using svglite(file ="a.pdf")...dev.off()

from cellchat.

@chuiqin It looks like your R does not support 'Arial' font style when doing plotting. Can you google such issue based on your system of the computer as I did not hear of such issue from other users? The extrafont package is available here. In addition, please try save the plot using svglite(file ="a.pdf")...dev.off()

Thank you very much!
You're right!
When I change my code:
`library(svglite)

svglite(file = "pathway.svg", width=10, height=10)

netVisual_aggregate(cellchat, signaling = pathways.show, vertex.receiver = c(1,2,3,5), vertex.size = groupSize)
dev.off()`
It‘s surperised that the picture can created correctly!
Thank you very much for your help again!

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Well, I got this error again .I have no idea about that how can I save the picture with the pdf format. who can help me ?

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@wuzhigui Have you tried svglite(file ="a.pdf")...dev.off() or saving as .svg file?

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Hi @Xethic , thank you so much for sharing this!

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I can't use netVisual_aggregate to get the graphics I want。I hope to get the following figure：

However, I always get such a circle

Can you help me, thank you~

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@Aby-GGG You should set 'layout = "hierarchy"'.

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