Baby-233 / Single-Cell_umap_tsne

scanno

install

install.packages(c('Seurat', 'dplyr', 'ggplot2', 'RColorBrewer'))

# install.packages("devtools")
devtools::install_github("sajuukLyu/ggunchull", type = "source")
install.packages("ggh4x")
install.packages("shadowtext")

devtools::install_github('seqyuan/annnosc')

example

现在只有一个画降维图的函数plot_dim，后续根据需求更新集成发表级函数。

library(annosc)
library(ggplot2)
library(Seurat)
library(dplyr)

rds <- readRDS('ifnb.rds')
Idents(rds) <- [e-mail]$seurat_annotations

plot_dim(rds, fill=TRUE)

plot_dim(rds, fill=NA, show.cls=c("CD4 Naive T", "CD14 Mono"))

plot_dim(rds, fill=TRUE, show.cls=c("T activated", "CD14 Mono"))

plot_dim(rds, fill=NA)

plot_dim(rds, fill=TRUE, show.pt=FALSE)

plot_dim(rds, fill=NA, show.pt=FALSE)

plot_dim(rds, reduction="pca")