一、安装

1、conda install -c conda-forge umap-learn

2、进入R：

devtools::install_github("ropenscilabs/umapr")

library(umapr)

提示：

Warning message:

Python not installed

Please install anaconda or miniconda

https://conda.io/projects/conda/en/latest/user-guide/install/index.html

Warning message:

umap-learn module is not installed

Please run one of the following:

conda install -n r-reticulate -c conda-forge umap-learn

conda activate r-reticulate; pip install umap-learn

解决：

library(reticulate)

py_available(） #结果若为FALSE则说明未安装python或python路径不在R的搜索路径中。

use_python("/root/miniconda2/envs/r-reticulate/bin/python", required = T)  #填写自己的python路径

二、绘图

library(reticulate)

use_python("/root/miniconda2/envs/r-reticulate/bin/python", required = T)

library(umapr)

library(dplyr)

library(magrittr)

library(ggplot2)

library(ggsci)

df <- read.table("/.../smart_seq_scaled_t.csv",sep=",", head=T, row.names=1)

df2 <- apply(df,1,as.numeric)

day <- read.table("/../day_info",sep="\t",row.names=1,head=T)

embedding <- umap(df2,n_neighbors=7L,min_dist =0.6,metric="braycurtis")

p <- embedding %>%

  mutate(days =day$days) %>%

  ggplot(aes(UMAP1, UMAP2, color = days)) + geom_point() + ggtitle("neighbors7_min_dist0.6_braycurtis") + scale_color_lancet() + 

theme(panel.grid=element_blank(),panel.background=element_rect(fill='transparent', color='black'),  plot.margin = unit(c(0.2, 0.2, 0.2, 0.2), "inches"), plot.title = element_text(hjust = 0.5, vjust =4,size=20,face = "bold"), legend.title = element_blank(), axis.text = element_text(colour = "black",face="plain",size=15), axis.title = element_text(colour = "black",face="plain",size=15), axis.line = element_line(colour = "black",size = 0.5), axis.ticks = element_line(colour= "black",size=0.5),legend.key = element_rect(fill='transparent', color='transparent'), legend.key.size = unit(0.2,"inches"), legend.text = element_text(colour = "black", face="plain", size=13))

ggsave("/.../neighbors7_min_dist06_braycurtis.png",p)

ggsave("/.../neighbors7_min_dist0.6_braycurtis.pdf",p)

三、结果