/CellMarkerR

CellMarkerR is a localized tool that includes two core drawing functions. These functions are based on the database that is publicly available on the CellMarker website.

Primary LanguageRGNU General Public License v3.0GPL-3.0

CellMarkerR

Description

CellMarkerR is a localized tool that includes two core drawing functions. These functions are based on the database that is publicly available on the CellMarker website.(http://bio-bigdata.hrbmu.edu.cn/CellMarker/CellMarkerSearch.jsp)

Getting Started

Recommend R language >= 3.6

Step.1 Install package dependencies

(Option A) Use R language code to install dependent packages.

# install.packages()
install.packages(c("plotly","htmlwidgets","wordcloud2","openxlsx"))

# BiocManager::install()
if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")
BiocManager::install(c("plotly","htmlwidgets","wordcloud2","openxlsx"))

(Option B) Use conda to install dependent packages.

conda install -c conda-forge r-plotly r-htmlwidgets r-wordcloud2 r-openxlsx

Step.2 Install the package

(Option A) Install the package directly from local.

install.packages("./CellMarkerR_1.0.0.tar.gz",repos=NULL,type="source")

(Option B) Install the package directly from github using the devtools package.

devtools::install_github("KIRA2ZERO/CellMarkerR")

Step.3 Library the package and initialize instance object

library(CellMarkerR)
CellMarker = CellMarkerR$new()

Step.4 Use R6 class methods

# viewMarker
CellMarker$viewMarker(marker="CD4")
CellMarker$getViewMarkerChartResult()
CellMarker$getViewMarkerTableResult()
CellMarker$saveViewMarkerChartResult(filePath) 
CellMarker$saveViewMarkerTableResult(filePath)

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# viewCell
CellMarker$viewCell()
CellMarker$getViewCellChartResult()
CellMarker$getViewCellTableResult()
CellMarker$getViewCellRankResult()
CellMarker$saveViewCellChartResult(filePath) 
CellMarker$saveviewCellTableResult(filePath) 
CellMarker$saveviewCellRankResult(filePath)

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