Prof. Jean Fan
Prof. Jean Fan
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Dear professor: How do I make high quality figures for my scientific publication? #tutorial #phdlife
Students in my lab requested a video tutorial on how to make high quality figures for our scientific publications, so I figured why not make the tutorial available to everyone.
Figures that are polished and well-designed can communicate complex ideas more quickly and efficiently. In this video, I go through the process of making a high quality publication-ready figure and narrate my general process, also summarized below:
Step 0: Make a mockup th-cam.com/video/L9qo2XZiQ4Y/w-d-xo.html
Step 1: Create vectorized versions of all figure panels th-cam.com/video/L9qo2XZiQ4Y/w-d-xo.html
Step 2: Combine your figure panels in a vector graphics software th-cam.com/video/L9qo2XZiQ4Y/w-d-xo.html
Step 3: Make sure everything is labeled and legible th-cam.com/video/L9qo2XZiQ4Y/w-d-xo.html
Step 4: Use visual similarity, proximity, and other Gestalt principles to enhance salience th-cam.com/video/L9qo2XZiQ4Y/w-d-xo.html
Step 5: Minimize distractions like multiple fonts or stroke weights th-cam.com/video/L9qo2XZiQ4Y/w-d-xo.html
Step 6: Balance use of white space and iterate as needed th-cam.com/video/L9qo2XZiQ4Y/w-d-xo.html
Try it out for yourself!
Links to software, programs, resources, and papers referenced in the video:
- Data visualization theory: jef.works/genomic-data-visualization-2024/course/1-data-visualization-theory/
- Figure style guide: jef.works/blog/2019/07/19/figure-style-faux-pas/
- STdeconvolve R package: github.com/JEFworks-Lab/stdeconvolve
- Scatterbar R package: github.com/JEFworks-Lab/scatterbar
- Affinity Designer Software: affinity.serif.com/en-us/designer/
- Inkscape Software: inkscape.org/
- Gestalt Principles: sketchplanations.com/gestalt-principles
- Example shown from our Miller et al paper: www.nature.com/articles/s41467-022-30033-z
- Example shown from our Clifton, Anant, et al paper: www.nature.com/articles/s41467-023-43915-7
- Example shown from our Aihara et al paper: academic.oup.com/bioinformatics/article/40/7/btae412/7696710
มุมมอง: 1 950

วีดีโอ

Navigating Healthcare Costs in America: struggle with me to shop for medical services using CMS TiC
มุมมอง 21116 ชั่วโมงที่ผ่านมา
For my European/non-American colleagues: come on a journey with me as I navigate healthcare costs in America and struggle to figure out which hospital I should go to to get a urinalysis using the shoppable medical services prices that hospitals have to make available now due to the Center for Medicare and Medicaid's Transparency in Coverage Final Rule! Skip to parts of interest: - Identifying a...
Gene count normalization in single-cell imaging-based spatially resolved transcriptomics
มุมมอง 8833 หลายเดือนก่อน
I'm learning how to give record my scientific talks from home. This video is an abbreviated version of invited scientific talks I have presented and continue to present at various scientific conferences for our work on gene count normalization in single-cell imaging-based spatially resolved transcriptomics. To learn more about our work developing computational methods for analyzing spatially re...
What is a university and who should it serve? | a short film
มุมมอง 7487 หลายเดือนก่อน
At this critical moment in history, with world-wide protests on university campuses, I ask my fellow members of the university to reflect: what is a university and who should it serve? Full reflection: jean.fan/2024/05/12/what-is-a-university.html Transcript What is a university? And who does it serve? Is it an institution of higher education, Serving the learning goals of the next generation, ...
Bioinformatics Live Coding Session - alignment of spatial transcriptomics data using STalign
มุมมอง 1.7K11 หลายเดือนก่อน
I record myself coding to perform an exploratory analysis where I structurally align a single-cell resolution spatial transcriptomics dataset profiled by the Xenium technology with a multi-cellular pixel resolution spatial transcriptomics profiled by the Visium technology from 10X Genomics of two serial breast cancer tumor tissue sections using our lab's bioinformatics Python tool STalign. I ho...
Teaching Statement | a short film
มุมมอง 1.8Kปีที่แล้ว
Every year, I give my lab (and myself) time off for what I call a "mini-sabbatical." Much like a typical sabbatical, my students are encouraged to use this time to travel, decompress, and/or pursue creative endeavors outside of their regular work/studies. The duration of the mini-sabbatical has varied from year to year but has spanned 2 to 6 weeks. It is announced in advance so everyone can coo...
10x Visium spatial transcriptomics data analysis with STdeconvolve in R
มุมมอง 4.7Kปีที่แล้ว
I'm trying out different video styles to teach students about bioinformatics analyses for spatially resolved transcriptomics data. In previous videos, I recorded myself live-coding and narrating through all my thought processes, mistakes, and troubleshooting. Now, I'm trying out sped-up versions. So in this video, I speed through coding a bioinformatics analysis in the R programming language to...
Live R Coding Session - normalizing spatial transcriptomics data for clustering vs deconvolution
มุมมอง 1.1Kปีที่แล้ว
We recently developed a computational method for analyzing multi-cellular pixel-resolution spatial transcriptomics (ST) data called `STdeconvolve` that recovers the proportion of cell types comprising each multi-cellular spatially resolved pixel along with each cell types' putative transcriptional profile without reliance on external single-cell transcriptomics references. More details regardin...
Live R Coding Session - single cell spatial transcriptomics data visualization in base R
มุมมอง 4.4Kปีที่แล้ว
I record myself coding in the R programming language to perform an exploratory bioinformatics analysis of single cell resolution spatial transcriptomics data in (almost entirely) base R ie. without reliance on additional external packages. This is in preparation for my upcoming Genomic Data Visualization course to help ensure that what I'll be asking students to do is indeed feasible. Some pote...
Live R Coding Session - Spatial transcriptomics data analysis with STdeconvolve and SpotClean
มุมมอง 4.8K2 ปีที่แล้ว
I record myself coding in the R programming language to perform an exploratory bioinformatics analysis of multi-cellular pixel resolution spatial transcriptomics Visium dataset from 10X Genomics using STdeconvolve with SpotClean preprocessing. I hope this will help give students a sense for how I would go about doing an exploratory bioinformatics data analysis, the kinds of challenges I often f...
Reference-free cell type deconvolution of spatial transcriptomics data with STdeconvolve
มุมมอง 2.4K2 ปีที่แล้ว
Reference-free cell type deconvolution of spatial transcriptomics data with STdeconvolve
Learn about spatially resolved transcriptomics through the highschool summer ISPEED program at JHU
มุมมอง 1.1K2 ปีที่แล้ว
Learn about spatially resolved transcriptomics through the highschool summer ISPEED program at JHU
Summarize for a 2nd grader: Spatial transcriptome profiling by MERFISH
มุมมอง 5892 ปีที่แล้ว
Summarize for a 2nd grader: Spatial transcriptome profiling by MERFISH
RNA-velocity informed embeddings for visualizing cellular trajectories with VeloViz
มุมมอง 6343 ปีที่แล้ว
RNA-velocity informed embeddings for visualizing cellular trajectories with VeloViz
Spatial transcriptome profiling by MERFISH reveals subcellular RNA compartmentalization
มุมมอง 3.8K3 ปีที่แล้ว
Spatial transcriptome profiling by MERFISH reveals subcellular RNA compartmentalization
HoneyBADGER links transcriptional and genetic intratumoral heterogeneity w/ single cell RNA-seq data
มุมมอง 7544 ปีที่แล้ว
HoneyBADGER links transcriptional and genetic intratumoral heterogeneity w/ single cell RNA-seq data
Pathway and Gene set OverDispersion Analysis characterizes single cell transcriptional heterogeneity
มุมมอง 1.2K4 ปีที่แล้ว
Pathway and Gene set OverDispersion Analysis characterizes single cell transcriptional heterogeneity

ความคิดเห็น

  • @sachalhussain5674
    @sachalhussain5674 5 ชั่วโมงที่ผ่านมา

    Thank you for sharing

  • @salarahmad-t2k
    @salarahmad-t2k 13 ชั่วโมงที่ผ่านมา

    Millions worth! Concise .

  • @SecundinoRodriguez-uu8vq
    @SecundinoRodriguez-uu8vq วันที่ผ่านมา

    Hi, Can we use Photoshop instead of Illustrator?

  • @petert888
    @petert888 2 วันที่ผ่านมา

    Love the video! Do you ever use {patchwork} or other packages to assemble multi-panel figures in R? It seems like once you move to Affinity reproducibility is lost.

  • @ilyasimutin
    @ilyasimutin 2 วันที่ผ่านมา

    This is incredible! Finding such high-quality tutorials is a real challenge.

  • @chia-lungwu4998
    @chia-lungwu4998 2 วันที่ผ่านมา

    Thanks so much for sharing! This is extremely helpful!!

  • @AbdulManan-ob3xj
    @AbdulManan-ob3xj 3 วันที่ผ่านมา

    Impressive :) Thanks a lot

  • @najibabdellaoui6442
    @najibabdellaoui6442 3 วันที่ผ่านมา

    thank a lot for the tutorial

  • @jungsukim3395
    @jungsukim3395 3 วันที่ผ่านมา

    Very helpful for my lab members! Thanks a lot!!!

  • @Themanintheredcoat
    @Themanintheredcoat 15 วันที่ผ่านมา

    Innovative idea. Mind if I steal it?

  • @BioJack_Academy2811
    @BioJack_Academy2811 2 หลายเดือนก่อน

    Thank you❤

  • @44eee44
    @44eee44 3 หลายเดือนก่อน

    The tutorial is hard to follow. There should be wrapper functions handles Seurat objects.

  • @garrick2781
    @garrick2781 4 หลายเดือนก่อน

    Thanks for the video, for imaging-based SRT techniques such as Stereo-seq where they capture the entire transcriptome, is it safe to assume that tranditional library size normalization is appropriate?

    • @JEFworks
      @JEFworks 3 หลายเดือนก่อน

      We generally consider current SRT techniques to be either imaging-based (including MERFISH, Xenium, STARmap, etc as discussed in this video) or sequencing-based (including Stereo-seq, Slide-seq, Visium, etc). For SRT techniques that provide full transcriptome profiling (including most sequencing-based SRT techniques), the assumptions underlying library size normalization should be satisfied.

  • @Brickkzz
    @Brickkzz 4 หลายเดือนก่อน

    Great content, but please get a better audio setup

  • @pent1162
    @pent1162 4 หลายเดือนก่อน

    Thanks for sharing it, but the echo is too severe, making it difficult to hear clearly. Because the background is dark, the icon may too dim to see clearly. Appreciated your sharing again.

    • @Trezzon
      @Trezzon 4 หลายเดือนก่อน

      Use the Closed Captioning.

  • @Life_of_Pal
    @Life_of_Pal 5 หลายเดือนก่อน

    Thank you, Jean.

  • @ruminationstation4200
    @ruminationstation4200 6 หลายเดือนก่อน

    Clever twist.

  • @AA-md7bt
    @AA-md7bt 6 หลายเดือนก่อน

    Disappointing!!

  • @RayY-r4j
    @RayY-r4j 6 หลายเดือนก่อน

    Nice glasses❤

  • @estebanelias6958
    @estebanelias6958 6 หลายเดือนก่อน

    Does it work with Geomx data?

  • @krazYFaic
    @krazYFaic 7 หลายเดือนก่อน

    Whatever it is, it's not worth it anymore.

  • @mohadesehzaree4918
    @mohadesehzaree4918 8 หลายเดือนก่อน

    Thank you Prof. Fan. I got the below error when tried to run "decont_obj <- spotclean(mbrain_obj)" Warning: No layers found matching search pattern provided Error in match.arg(arg = method, choices = names(x = methods)) : 'arg' should be one of ". Could you please help me?

  • @0jaxay0
    @0jaxay0 8 หลายเดือนก่อน

    nice

  • @TIANTHINGJESTLINNG
    @TIANTHINGJESTLINNG 8 หลายเดือนก่อน

    Omg thank you Prof Jean Fan. As a student self learning bioinformatics for my research, I have really learnt a lot from watching your video as you work through the data with full details on how to troubleshoot etc. I hope you continue making live sessions!

  • @InquilineKea
    @InquilineKea 8 หลายเดือนก่อน

    Deconvolution of cell type contributions of pixelsWITHIN a cell?

  • @SonkMc
    @SonkMc 9 หลายเดือนก่อน

    Wish the world had much many professors like you! And also lovely doggos

  • @amitozazad1584
    @amitozazad1584 9 หลายเดือนก่อน

    Man I wish my professors were so cool!

  • @donnizhang5960
    @donnizhang5960 10 หลายเดือนก่อน

    !!! love this

  • @donnizhang5960
    @donnizhang5960 10 หลายเดือนก่อน

    thought provoking!

  • @MohamedAlkassemAlosman
    @MohamedAlkassemAlosman 10 หลายเดือนก่อน

    Great video! Thank you so much!

  • @Mayling54
    @Mayling54 11 หลายเดือนก่อน

    OMG Professor Fan!! You look so good here 😊

  • @izabela8725
    @izabela8725 ปีที่แล้ว

    great videos, very helpful! Will you by any chance also analyse Xenium spatial transcriptomics data from 10X?

  • @ThạchCNCPhanVăn
    @ThạchCNCPhanVăn ปีที่แล้ว

    Can you teaching how to integrating Spatial Transcriptomic with multiple single cell data, Thank you!

  • @fyzen568
    @fyzen568 ปีที่แล้ว

    Really inspiring, "And when the occasion arises, people must be able to think and to decide to disobey"

  • @ThạchCNCPhanVăn
    @ThạchCNCPhanVăn ปีที่แล้ว

    Thank so much for your video, It really helpfull to me. I hope you could pub more video about Spatial Transcriptomics

  • @relaxenjoy9817
    @relaxenjoy9817 ปีที่แล้ว

    Thank you Does it mean, that if one is using SpaceRanger v2 to process the sequencing Visium data, using STdeconvolve in R is unnesecary afterwards? best

  • @mcmacshalfilya
    @mcmacshalfilya ปีที่แล้ว

    Darn. She said the dreaded 'H' word..😒

  • @mcmacshalfilya
    @mcmacshalfilya ปีที่แล้ว

    Professor JEAN U are such a DREAM✨

  • @hatawa6135
    @hatawa6135 ปีที่แล้ว

    is it correct to say: "what "Genes" are localized to subcellular compartments"? I understand the definition of a Gene as DNA fragment, and the localization you are referring to is "Gene expression" or RNA, as opposed to "genes".

  • @koustavroy350
    @koustavroy350 ปีที่แล้ว

    Hello Dr. Fan, Thank you so much for quality videos. Could you please teach how to perform DEG analysis in two different spatial transcriptome datasets?

  • @Brickkzz
    @Brickkzz ปีที่แล้ว

    Having a video like this but in Python would be great!

  • @haohuifang8674
    @haohuifang8674 ปีที่แล้ว

    Coollll! Benefits a lot from your course. Keep going Dr. Fan!

  • @veki2630
    @veki2630 ปีที่แล้ว

    :(

  • @huishanliu6307
    @huishanliu6307 ปีที่แล้ว

    Nope. He is too demanding.

  • @aygulminnegalieva4368
    @aygulminnegalieva4368 ปีที่แล้ว

    This is so unfair 😢

  • @jacklee4356
    @jacklee4356 ปีที่แล้ว

    He does not deserve your effort and the spent IO/threads.

  • @thedoge9590
    @thedoge9590 ปีที่แล้ว

    Could have just said day in the life of a professor....

  • @juliangrandvallet5359
    @juliangrandvallet5359 ปีที่แล้ว

    Thank you, Dr., Please keep doing these videos! they are very helpful

  • @taobohu1402
    @taobohu1402 ปีที่แล้ว

    Hi Prof. Fan, thank you so much, very nice tools! And very cute dog :)

  • @arianescajeda639
    @arianescajeda639 ปีที่แล้ว

    I love your videos. 😊