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
