PBMC 3k tutorial

Hai Nguyen

2023.06.20

This tutorial will use PBMC analysis data from Seurat.

To get a complete description of the experiment, refer here

We assume that all dependent packages are already installed. see How to install CellEnrich document.

Required Data

Pre-processed data is included in GitHub repository.

Filename Parameter Type
pbmcData.RData CountData dgCMatrix
pbmcClustinfo.RData GroupInfo Character

Run

with these Codes, users can see an interactive shiny page.


# Download data, if not downloaded
CellEnrich::DownloadData()

load("pbmcData.RData")
load("pbmcClustInfo.RData")

CountData <- pbmcData
GroupInfo <- pbmcClustInfo

# This will run CellEnrich
CellEnrich(CountData, GroupInfo)

Result

Set options before starting CellEnrich.

Possible options are :

  • Strategy for Differential Expressed Genes.
  • Plot Options
  • Gene-set and their size cutoff to be used in the analysis.

After a few minutes, the analysis result will appear.

used Test environment :

  • OS : Ubuntu 22.04 LTS
  • CPU: iAMD® Ryzen 9 5950x 16-core processor × 32
  • RAM: 64GB

CellEnrich consists of 5 modules.

1. Parameter Selection

2. Scatter Area

The left plot is a scatter plot created with t-SNE or U-MAP and ggplot2 that the user selected in the option.

  • In this tutorial, the scatter plot is the t-SNE result.

  • this scatter plot can be emphasized with 3 buttons:

    1. CELL GROUPS button ( default ) will colorize as group information.

    2. FREQUENCY button will colorize frequently enriched cells in each group.

    3. ODDS RATIO button will colorize the enriched cell in each group with the highest odds ratio.

The right plot is a histogram plot created with high charter to see a distribution of Group / Cell labels.

  • In this tutorial, 9 group exists.

User can download both result with the Save button (LEFT) and Export options at the right top (RIGHT).

3. Pathways Module

This pathway module will show significant pathways for each group in table format.

To use emphasize feature, a user should clear the sortable list with the CLEARLIST button.

For each group, only 1 pathway can be selected for emphasis in a scatter plot.

After clicking the ‘EMPHASIZE’ button, top cell enriched by the selected pathways will be shown.

4. BiPlot Module

This section shows the BiPlot presentation of the correlation between categories and top significant pathways.

User can check the BiPlot under the perspective of FREQUENCY (above) or ODDS RATIO (below).

5. Marker Module

This marker module will show Differentially Expressed genes in the following:

  1. Each group ( using findMarker in scran )

  2. Each group and pathway-specific ( using Fisher’s exact test )

License

Developers

  • Hai Nguyen
    Author, maintainer