R Series #21 Data Visualization: How to do Chord Diagram (Circular plot) using R -w/ the code-

This video is a tutorial for programming in R Statistical Software for beginners and it's simply explained with a live workshop on RStudio.
In this video, you will learn how to do Chord Diagram in R
The codes are available on my R blog below:
bioinfo4all.wo...
The link for the paper:
doi.org/10.339...
#Learn R in a simple and systematic way
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[@dr.ozgekahramanilkkan3499]

I have been searching for a month for this chord diagram... thanks a lot

[@bioinformaticsforall901]

You are welcome 😊

[@prateekyadav7679]

Thank you for this tutorial. Is it possible to add more tracks to this chord diagram to convey additional information?

[@ElisaJosefaGonzalezUgalde]

Thank you so much for this video! I just want to ask, do you know if the figure of Soldatou et al. 2021, in order to have those "lines", was edited in Photoshop or something like that? My labels are very long and they get cutted, so i want to do something like that figure :(

[@cecio2323]

Thank you very much, it was extremely useful!

[@bioinformaticsforall901]

You are very welcome Odette:) I am happy to hear that :)

[@KN-tx7sd]

can we add bar charts and heat maps to the chord diagram

[@smraza9]

Thankyou so much for this video you helped me alot. There is a correlation map that I am unable yo make and find way to make it can you make a tutorial for it. I can share the pubmed link to the article? I would be much obliged

[@mohnadabdalla1207]

Thank you so much

[@raheelshahzad1423]

Thank you so much for such a wonderful lecture. I would like to ask how you design your slides ? because your presentation is wonderful on slides. thank you once again 🏆

[@altafhussainnarejo6685]

Could u tell me how to add more column file in excel CSV in R studio. I need you help.

[@carlossalasmacias]

Hello, thanks for the contribution, it has been very useful. I am working with species, I need the row labels to be italicized, how can I achieve this?

[@Purnima_Chowdhury]

i cannot find chordDiagram in R.. Can anyone help

[@santhanagopalakrishnangopa4650]

is there a function to reduce the chord diameter?, like make a small chord circle ,cuz my data names are lengthier !. Suggestions would be helpful.

[@QuentinAndres06]

amazing

[@bioinformaticsforall901]

Glad you think so!

[@francescaf6903]

Thank you so much for your video! Is there a way to only display the categories once on the plot? I have the same categories on the row and column names for the matrix. Is there a way to show only one set of categories? thank you!

[@bioinformaticsforall901]

Yes you can! If the row names and column names are the same, chordDiagram() function will show only one.

[@francescaf6903]

@@bioinformaticsforall901 awesome it worked, thank you so much!!!

[@jaimeojedav]

@@bioinformaticsforall901 I have the same issue with categories that are the same in row and column, but the message says "Error in abs(mat) : non-numeric argument to mathematical function". Please, a help

[@sajeevan81]

Thank you very much for the video. I have an issue. I am not able to give the respective colors for my strain with the following. It is giving again random colors for my strains and the grey ones are showing in the diagram. Also, how to give the labels without the interconnecting (Organonitrogen.compound.biosynthetic.process) dots? Can you kindly help me? col = c(Magnum.bonum.18.hpi="#330033" , Désirée.18.hpi="#FF3300" , Kuras.18.hpi="#3399CC" , Organonitrogen.compound.biosynthetic.process = "grey" , Cellular.amide.metabolic.process = "grey" , Amide.biosynthetic.process = "grey" , Peptide.metabolic.process = "grey") .

[@nehajha2312]

Thanku so much, you made so easy. I want to ask about the genes and chromosome relation with disease. How we are going to represent it

[@bioinformaticsforall901]

You are welcome :) there are so many ways to visualize the data and its very difficult to tell you which way its the best without looking at the data, circular plots, pca and heatmaps are all good for such tasks.

[@saphhire_tales]

> library(circlize) > data View(data) > data1 chordDiagram(data1) Error in abs(mat) : non-numeric argument to mathematical function Hi I am getting above error , can anyone help me plz

[@judethaddeausadjei8989]

Me too

[@khanmohdsarim]

I am getting this error when generating chordDiagram Error in abs(mat) : non-numeric argument to mathematical function

[@saphhire_tales]

did you get the answer of this error?

[@Dr.munna89]

Sir I have send an email to you about a problem I faced in chord diagram. I have used your code.

[@hollyb1465]

Hello, I am also getting an issue when trying to apply 'circos.trackPlotRegion(track.index = 2, panel.fun = function(x, y) { xlim = get.cell.meta.data("xlim") ylim = get.cell.meta.data("ylim") sector.name = get.cell.meta.data("sector.index")' I get an error message: 'Error: Incomplete expression:' Do you have any guidance on how to fix this? Thanks!

[@bioinformaticsforall901]

Without having the data is very difficult to know the problem. If you follow everything in the video and organized your data according to how I did it in the video, the code should work.

[@hollyb1465]

​@@bioinformaticsforall901 Hi! Its working now, I realised I wasn't running the whole expression at the same time - thank you so much your videos are very helpful

[@bioinformaticsforall901]

You are welcome Holly B :)

[@azzeddinereghais7494]

Please, I have an error with the following code when trying it #add the labels and axis circos.trackPlotRegion(track.index = 2, panel.fun = function(x, y) { xlim = get.cell.meta.data("xlim") ylim = get.cell.meta.data("ylim") sector.name = get.cell.meta.data("sector.index") I followed the same steps that I talked about I hope provide me a solution to this dilemma

[@bioinformaticsforall901]

Hi Azzeddine! I used the code yesterday. It was working fine. Can you tell me what R is returning when you fun the command above?

[@azzeddinereghais7494]

@@bioinformaticsforall901 A "X" sign appears there on the left It does not apply the code I guess the problem is in copying the code Kindly rewrite me here in the comment Thank you

[@azzeddinereghais7494]

Well explanation and great job, I hope there are videos explaining how to apply it in PCA CAH

[@bioinformaticsforall901]

Thank you Azzeddine :) I will look into it if I can do it, otherwise you can find such tutorial on other KZbin channel.

[@azzeddinereghais7494]

@@bioinformaticsforall901 The way you explain it is really simple. I would love to follow you I wish you all the best

[@bioinformaticsforall901]

Thank you Azzeddine:)

[@zeinabourhane874]

Thank you :)

[@bioinformaticsforall901]

You are welcome Zeina :)

[@zeinabourhane874]

Hello, my first col is the code of genes ( i have 240) the second col is the function of each gene ( i have in total 10 differents functions), is there a way to plot the functions ?? because if remove the first col, i will have a row names repetition in my data set.

[@bioinformaticsforall901]

One idea is to color those that have same function with same color so you can write in the explanation for example: Purple color are genes responsible for apoptosis.