This is a test version of Biostars. For the public version, visit https://www.biostars.org.
question about seurat figure PC_heatmap

Hello,

Does anyone know what is the mean of the following figure?

I know it is heatmap, what is the meaning of four blocks?

It comes from a single-cell RNA-seq, Seurat package.

Thanks in advance for any help!

Best,

Yue

seurat23

rna-seq
• 4,044 views • link
updated by jared.andrews07 jared.andrews07 • written by yueli7 yueli7

Maybe you would like to give a more meanigful title?

• 0 views • link
written by Medhat Medhat

Hello, Medhat,

Already change the title.

Thank you!

Best,

Yue

• 0 views • link
written by yueli7 yueli7

1 answer

It just shows the genes that compose your top principal component (i.e. explain the most amount of variability within your data), along with their principal components scores sorted by cells.

The DimHeatmap function is geared to help you define how many principal components in your data actually have significant variability to be worth including in additional analysis and dimensionality reductions like TSNE and UMAP.

• 0 views • link
written by jared.andrews07 jared.andrews07

Hello, jared.andrews07,

Thank you so much for your response!

Thank you again!

Best,

Yue

• 0 views • link
written by yueli7 yueli7

What about the colors. How do you interpret them?

• 0 views • link
written by rohitsatyam102 rohitsatyam102

Yellow is high, purple is low. At least by default. Color scale should always be posted with plot to make it easy to interpret.

• 0 views • link
written by jared.andrews07 jared.andrews07

Log in to answer this question.

More posts like this
  • enriched genes PPI network
    written by yueli7 yueli7
    Hello, I want to make a figure just like below Figure 1. I went to string database and made a search: https://string-db.org/cgi/input?sessionId=bHX2BS9VeUGo&input_page_show_search=on. The result just …
  • Frequency of the gene expression in Seurat
    written by yueli7 yueli7
    Hello, I can go through the Seurat all the code from here: https://satijalab.org/seurat/archive/v3.0/visualization_vignette.html. My question is: Is that possible that I can get the frequency …
  • phred score per base sequence quality
    written by yueli7 yueli7
    Hello, I have RNA sequencing data. After running FastQc, it comes out bad result. Do I need to fix it? Thanks in advance for any …
  • How to make protein table?
    written by yueli7 yueli7
    Hello, I have two matrix, and want to make a protein table. I used package of proteus from R. Thank you in advance for your …
  • Which package I can use in SILAC data?
    written by yueli7 yueli7
    Hello, I have a set of SILAC protein data which only has the value of the `Light/Heavy`. It has 12 columns and 6674 rows. Which …
  • separate the figure
    written by yueli7 yueli7
    Hello, I have figure like this: Ia that possible I can separate the figure into three: 1. healthy control, 2. mild, 3. severe? Thanks in …
  • what is the definition of "cell barcode collapsing"
    written by yueli7 yueli7
    Hello, What is the meaning of the following figure? Summay plot of cell barcode collapsing. Plot the original frequency of each cell barcode in the …
  • name of the figure
    written by yueli7 yueli7
    Hello, Everyone, Anyone know the name of the figure? Thanks in advance for any help! Best, Yue <img src="https://i.ibb.co/NZbSgDy/Screenshot-from-2019-12-12-15-56-59.png" alt="Screenshot-from-2019-12-12-15-56-59" border="0" />
  • question ablout seurat figure PC_contribution
    written by yueli7 yueli7
    Hello, Anyone now what is the mean of following figure? I know it is the PC_1, what is the number in x-axis? It comes from …
  • software that can draw this figure
    written by yueli7 yueli7
    Hello, Any one who can tell me which software can draw this figure? Thanks in advance! Yue <a href="https://imgbb.com/"><img src="https://image.ibb.co/cORhr8/Phospho_Site_Plus_01.png" alt="Phospho Site Plus 01" border="0" …