Package 'SeuratExplorer'

Title: An 'Shiny' App for Exploring scRNA-seq Data Processed in 'Seurat'
Description: A simple, one-command package which runs an interactive dashboard capable of common visualizations for single cell RNA-seq. 'SeuratExplorer' requires a processed 'Seurat' object, which is saved as 'rds' or 'qs2' file.
Authors: Yongchao Zhang [aut, cre] (https://github.com/fentouxungui)
Maintainer: Yongchao Zhang <[email protected]>
License: GPL (>= 3)
Version: 0.1.0
Built: 2025-03-14 04:50:36 UTC
Source: https://github.com/fentouxungui/seuratexplorer

Help Index


plot cell percentage barplot

Description

support facet, codes refer to: https://github.com/junjunlab/scRNAtoolVis/blob/master/R/cellRatioPlot.R, with modification

Usage

cellRatioPlot(
  object = NULL,
  sample.name = NULL,
  sample.order = NULL,
  celltype.name = NULL,
  celltype.order = NULL,
  facet.name = NULL,
  facet.order = NULL,
  col.width = 0.7,
  flow.alpha = 0.25,
  flow.curve = 0,
  color.choice = NULL
)

Arguments

object

an Seurat object

sample.name

x axis

sample.order

order for x axis

celltype.name

column fill by

celltype.order

order for fill by

facet.name

column name for facet

facet.order

the order for facet

col.width

column width, from 0-1

flow.alpha

transparency for flow

flow.curve

curve for flow

color.choice

color choice for fill

Value

a ggplot2 object

Examples

#NULL

generate the body UI for each menu item specified in explorer_sidebar_ui

Description

generate the body UI for each menu item specified in explorer_sidebar_ui

Usage

explorer_body_ui(tab_list)

Arguments

tab_list

a tag list for the body UI of shiny dashboard

Value

a filled tag list for body UI

Examples

tab_list <- list()
tab_list <- explorer_body_ui(tab_list = tab_list)

server side functions related to explorer_sidebar_ui

Description

server side functions related to explorer_sidebar_ui

Usage

explorer_server(input, output, session, data, verbose = FALSE)

Arguments

input

server input

output

server output

session

server session

data

the Seurat object and related parameters

verbose

for debug use

Value

server side functions related to explorer_sidebar_ui


some menu items of the dashboard sidebar

Description

to generate some menu items for the dashboard, which can be integrated to other packages, such as 'fentouxungui/SeuratExplorerServer' from github.

Usage

explorer_sidebar_ui()

Value

return some menu items for the dashboard

Examples

explorer_sidebar_ui()

getColors

Description

getColors

Usage

getColors(color.platte = NULL, choice = NULL, n = NULL)

Arguments

color.platte

predefined color list

choice

color name

n

how many colors to return

Value

a color list

Examples

# null

Launch shiny app

Description

Launch shiny app

Usage

launchSeuratExplorer(verbose = FALSE)

Arguments

verbose

for debug use

Value

In-browser Shiny Application launch

Examples

if(interactive()){launchSeuratExplorer()}

Server

Description

Server

Usage

server(input, output, session)

Arguments

input

Input from the UI

output

Output to send back to UI

session

from shiny server function

Value

the server functions of shiny app


Find Top Genes by Cell

Description

for each cell, find genes that has high UMI percentage, for example, if a cell has 10000 UMIs, and the UMI percentage cutoff is set to 0.01, then all genes that has more than 10000 * 0.01 = 100 UMIs is thought to be the highly expressed genes for this cell.summary those genes for each cluster, firstly get all highly expressed genes in a cluster, some genes may has less cells, then for each gene, count cells in which this genes is highly expressed, and also calculate the mean and median UMI percentage in those highly expressed cells.

Usage

top_genes(SeuratObj, expr.cut = 0.01, group.by)

Arguments

SeuratObj

Seurat object

expr.cut

UMI percentage cutoff, in a cell, if a gene with UMIs ratio more than this cutoff, this gene will be assigned to highly expressed gene for this cell

group.by

how to group cells

Value

a data frame


UI

Description

UI

Usage

ui()

Value

the UI part of the shiny app

Examples

ui()