Package 'SeuratExplorer'

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,
  idents = 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
idents	idents used, default all idents
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()

---

Genes information extracted from genome gtf file

Description

A data set containing the gene information from species of human, mouse and fly.

Usage

GenesDB

Format

A list:

fly

a data frame, with columns: "Ensembl","Symbol", "EntrezID", "UniProt", "Name", "Alias"

mouse

a data frame, with columns: "Ensembl","Symbol", "MGI", "EntrezID", "UniProt", "Name", "Alias"

human

a data frame, with columns: "Ensembl","Symbol", "HGNC", "EntrezID", "UniProt", "Name", "Alias"

---

Helper function to extract counts matrix with proper handling

Description

Helper function to extract counts matrix with proper handling

Usage

get_counts_matrix(SeuratObj, assay = "RNA")

Arguments

SeuratObj	A Seurat object
assay	Assay name

Value

A counts matrix

---

Helper function to extract data matrix with proper handling

Description

Helper function to extract data matrix with proper handling

Usage

get_data_matrix(SeuratObj, assay = "RNA")

Arguments

SeuratObj	A Seurat object
assay	Assay name

Value

A data matrix

---

getColors

Description

getColors

Usage

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

Arguments

color.platte	predefined color list
choice	color name
n	how many colors to return

Value

a color list

Examples

# null

---

Helper function to join layers for Assay5 objects

Description

Helper function to join layers for Assay5 objects

Usage

join_layers_if_needed(SeuratObj, assay = "RNA")

Arguments

SeuratObj	A Seurat object
assay	Assay name

Value

Seurat object with joined layers

---

Launch shiny app

Description

used to launch the shiny app in a web browser.

Usage

launchSeuratExplorer(
  verbose = FALSE,
  ReductionKeyWords = c("umap", "tsne", "pca"),
  SplitOptionMaxLevel = 12,
  MaxInputFileSize = 20 * 1024^3,
  DemoDataURL =
    c("https://raw.githubusercontent.com/fentouxungui/SeuratExplorerServer/refs/heads/main/inst/extdata/source-data/fly/Rds-file/G101_PC20res04.rds",
    "https://drive.usercontent.google.com/download?id=1iscfl4zyNbtjAol0bwndnBI08MDcZvYE&export=download&authuser=0&confirm=t&uuid=6352f610-9125-4551-afaa-e1eedd15701c&at=AMrWOn0YlTymrOPO6Rb0GlFtJ07o%3A1790127440033",
    "https://www.daokedao.site/data/G101_PC20res04.rds"),
  DemoDataCacheDir = NULL,
  DemoDataMD5 = "e144cabc42684f037e60a603f74ed4f1"
)

Arguments

verbose	for debug use
ReductionKeyWords	key words used for prepare Reduction options
SplitOptionMaxLevel	max level cutoff for prepare Split options
MaxInputFileSize	set the limited upload file size
DemoDataURL	one or more URLs of the demo Seurat object downloaded by the "Download and Run a demo data" button. Multiple URLs are tried in order until one succeeds (primary, then backup)
DemoDataCacheDir	directory used to cache the downloaded demo data; if NULL, a per-user cache directory is used
DemoDataMD5	expected md5 checksum of the downloaded demo data; set to NULL to skip the integrity check

Value

In-browser Shiny Application launch

Examples

if(interactive()){launchSeuratExplorer()}

---

Create a collapsible parameter group for Plot Settings

Description

Creates a styled, collapsible parameter group for the Plot Settings sidebar. Clicking the header toggles visibility of the content area. The group preserves the existing color-coded left border styling.

Usage

param_group_collapse(id, title, icon_name, color = "#3b82f6", ...)

Arguments

id	A unique identifier for the collapse target (used as the div ID).
title	Character string for the group header title.
icon_name	Character string passed to shiny::icon().
color	Hex color string for the left border and title accent. Default: "#3b82f6".
...	UI elements to place inside the collapsible content area. Groups always start expanded.

Value

A shiny.tag div representing the collapsible parameter group.

---

extract the features from row names or annotation slot of assays

Description

extract the features from row names or annotation slot of assays

Usage

prepare_gene_annotations(obj, verbose = FALSE)

Arguments

obj	a Seurat object
verbose	whether output messages

Value

a list with data.frames

Examples

#NULL

---

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, percent.cut = 0.01, group.by, assay = "RNA")

Arguments

SeuratObj	Seurat object
percent.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
assay	which assay used

Value

a data frame

---

UI

Description

UI

Usage

ui()

Value

the UI part of the shiny app

Examples

ui()

---