scRNAtoolVis包使用：UMAP, featureplot,heatmap美化

corrschi發表於2024-04-04

參考原文連結：
https://mp.weixin.qq.com/s/K8FHv0dxriaGxKI0efRN5g
https://mp.weixin.qq.com/s/gtnYWJcUubNKT4SIldk9uQ

1.安裝

devtools::install_github('junjunlab/scRNAtoolVis')
library(scRNAtoolVis)

#過程報錯，需要首先安裝依賴包：magick
install.packages（"magick"）

#再次報錯，需要先安裝magick依賴的imagemagick
$conda install conda-forge::imagemagick

2.使用

#test data
library(scRNAtoolVis)

# load test data
test <- system.file("extdata", "seuratTest.RDS", package = "scRNAtoolVis")
tmp <- readRDS(test)

具體見最開始參考教程。自己使用的一個示例：

library(scRNAtoolVis)
png(paste0("featureplot-main_marker.png"), width = 18, height = 6, res = 400, units = "in")
# given a range to plot
p1 <- FeatureCornerAxes(object = MERGE,reduction = 'umap',
                        groupFacet = NULL,
                        relLength = 0.5,
                        relDist = 0.1,
                        features =c("CX3CR1","CLDN5","GFAP","PCDH15","MBP"),
                        # aspect.ratio = 1,
                        # themebg = 'bwCorner',#增加方框
                        minExp = 0,maxExp = 5,#設定最大和最小顯示值
                        show.legend=F #是否顯示圖例
                        )

p2 <- FeatureCornerAxes(object = MERGE,reduction = 'umap',
                        groupFacet = NULL,
                        relLength = 0.5,
                        relDist = 0.1,
                        features = c("SATB2", "SLC17A7","CAMK2A","GAD1","GAD2"),
                        # aspect.ratio = 1,
                        # themebg = 'bwCorner'
                        # show.legend=T #是否顯示圖例
                        minExp = 0,maxExp = 5#設定表達量最小和最大顯示值
                        )
# combine
cowplot::plot_grid(p1,p2,ncol = 1,align = 'hv') #上下兩行
# cowplot::plot_grid(p1,p2,ncol=2,align='hv') #兩列
dev.off()
                 

png(paste0("featureplot-neruon.png"), width = 9, height = 3, res = 400, units = "in")
# given a range to plot
FeatureCornerAxes(object = MERGE,reduction = 'umap',
                        groupFacet = NULL,
                        relLength = 0.5,
                        relDist = 0.1,
                        features =c("SNAP25", "STMN2", "RBFOX3"),
                        # aspect.ratio = 1,
                        # themebg = 'bwCorner'
)

dev.off()

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