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library(LTMGSCA)
library(Matrix)
library(dplyr)
library(ggplot2)
library(ggpubr)
library(Rtsne)
library(RColorBrewer)
library(KRLS)
library(RSpectra)
library(SwarmSVM)
library(reshape2)

### Read and preprocess 10X files
PBMC<-Read10X("GRCh38")
PBMC_meta<-Data_Meta(PBMC)

Error in colSums(MAT > 0) : 
  'x' must be an array of at least two dimensions

library(LTMGSCA)
library(Matrix)
library(dplyr)
library(ggplot2)
library(ggpubr)
library(Rtsne)
library(RColorBrewer)
library(KRLS)
library(RSpectra)
library(SwarmSVM)
library(reshape2)
PBMC<-Read10X("hg19")
PBMC<-as.matrix(PBMC)
PBMC_meta<-Data_Meta(PBMC)
Plot_Meta(PBMC_meta)
#ggsave("test_meta.png",width=4,height=4,dpi=300)
PBMC<-Data_subset(PBMC,PBMC_meta,nFeature.lower = 200,nFeature.upper = 2000,Counts.upper = 5000,Percent.mt.upper = 0.1)
str(PBMC_meta)
#List of 3
# $ nFeature  : Named num [1:2700] 781 1352 1131 960 522 ...
#  ..- attr(*, "names")= chr [1:2700] "AAACATACAACCAC" "AAACATTGAGCTAC" "AAACATTGATCAGC" "AAACCGTGCTTCCG" ...
# $ Counts    : Named num [1:2700] 2421 4903 3149 2639 981 ...
#  ..- attr(*, "names")= chr [1:2700] "AAACATACAACCAC" "AAACATTGAGCTAC" "AAACATTGATCAGC" "AAACCGTGCTTCCG" ...
# $ Percent.mt: Named num [1:2700] 0.03015 0.03794 0.00889 0.01743 0.01223 ...
#  ..- attr(*, "names")= chr [1:2700] "AAACATACAACCAC" "AAACATTGAGCTAC" "AAACATTGATCAGC" "AAACCGTGCTTCCG" ...
PBMC<-PBMC[rowSums(PBMC>0)>0.01*ncol(PBMC),]
PBMC<-NormalizeCount(PBMC)
Zcut_G<-log(Global_Zcut(PBMC))
head(Zcut_G)
#[1] 0
Gene<-"CCL5"
VEC<-PBMC[Gene,]
VEC_LTMG<-LTMG(VEC,Zcut_G,k=5)
plot_gene(VEC = VEC,Data_LTMG = VEC_LTMG,Zcut = Zcut_G)