In unistbig/CellEnrich: Pathway Enrichment Analysis, Visualize for Single Cell Data

knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>"
)

In this tutorial, we will use PBMC analysis data from Seurat.

To get full description about experiment, refer here

We assume that all dependent packages is 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, user can see 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 start CellEnrich.

Possible options are :

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

After 30 seconds ~ 1 min, analysis result will be appear.

used Test environment :

• OS : win 10
• CPU : i5-8400
• RAM : 16G

CellEnrich is consisted with 3 modules.

1. Plot Module

Left plot is scatter plot created with t-SNE or U-MAP and ggplot2 that user selected in option.

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

• this scatter plot can be emphasized with 4 buttons:

• TOCOLOR button ( default ) will colorize as group information.

• TOGRAY button will colorize all dots to gray color.

1. FREQUENT button will colorize frequently enriched cell in each group.

1. SIGNIFICANT button will colorize most significantly enriched cell in each group.

Right plot is histogram plot created with highcharter to see distribution of Group / Cell labels.

• In this tutorial, 9 group exists.

User can download both result with save button (LEFT) and export options in right top (RIGHT).

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2. Marker Module

This marker module will show Differentially Expressed genes in :

1. Each group ( using findMarker in scran )

2. Each group and pathway specific ( using fisher's exact test )

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3. Pathways Module

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

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

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

2 emphasize option can be used.

1. WITHOUTORDER : This will emphasize cells with selected pathway is enriched.

1. WITHORDER : This will emphasize cells with selected pathway is enriched. and also it will generate path based on order in sortable

Using SAVE button in pathways module, user can download pathway - group significance table.

unistbig/CellEnrich documentation built on July 27, 2020, 12:52 p.m.