| Title: | An 'Shiny' App for Exploring scRNA-seq Data Processed in 'Seurat' |
| Version: | 0.1.0 |
| 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. |
| License: | GPL (≥ 3) |
| Encoding: | UTF-8 |
| RoxygenNote: | 7.3.2 |
| Imports: | ggplot2, utils, Seurat, shiny, shinydashboard, DT, shinycssloaders, patchwork, tools, colourpicker, shinyWidgets, scales, SeuratObject, shinyjqui, shinyBS, ggalluvial, dplyr, ComplexHeatmap, qs2, circlize, reshape2, stats, htmltools |
| Depends: | R (≥ 4.1.0) |
| Suggests: | BiocManager, DESeq2, MAST, roxygen2, devtools |
| NeedsCompilation: | no |
| Packaged: | 2025-03-12 00:05:21 UTC; Xi_Lab |
| Author: | Yongchao Zhang [aut, cre] (https://github.com/fentouxungui) |
| Maintainer: | Yongchao Zhang <zhangyongchao@nibs.ac.cn> |
| Repository: | CRAN |
| Date/Publication: | 2025-03-13 13:10:05 UTC |
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()