## ----pre_install, eval = FALSE------------------------------------------------
#  if(!requireNamespace("BiocManager", quietly = TRUE))
#      install.packages("BiocManager")
#  # install from bioconductor
#  BiocManager::install(c('org.Mm.eg.db','multtest', 'org.Hs.eg.db','clusterProfiler','DEsingle', 'DrImpute', 'scater', 'scran'))
#  # install from cran
#  chooseCRANmirror()
#  BiocManager::install(c('devtools', 'AdaptGauss', "pheatmap", 'mixtools','MCL', 'anocva', "Polychrome", 'qgraph','Rtools','ggpubr',"ggraph", "Seurat"))
#  

## ----install_IRISFGM, eval= FALSE---------------------------------------------
#  BiocManager::install("IRISFGM")

## ----setwd, eval =TRUE, echo = TRUE-------------------------------------------
# dir.create("your working directory",recursive = TRUE)
# setwd("your working directory")
library(IRISFGM)

## ----input_h5, eval= TRUE, echo = TRUE----------------------------------------
# if you will use the ".h5" as input file, please uncomment the following command.
# input_matrix <- ReadFrom10X_h5("dir_to_your_hdf5_file")

## ----input_10x, eval = TRUE, echo = TRUE--------------------------------------
# if you will use the 10x folder as input file, please uncomment the following command.
# input_matrix <- ReadFrom10X_folder("dir_to_10x_folder")

## ----txt, eval= TRUE, echo = TRUE---------------------------------------------
InputMatrix <- read.table(url("https://raw.githubusercontent.com/BMEngineeR/IRISFGM-data/main/Data/Yan_expression.txt"),
                          header = TRUE, 
                          row.names = 1,
                          check.names = FALSE)

## ----create_object, eval= TRUE, echo = TRUE,message=TRUE----------------------
set.seed(123)
seed_idx <- sample(1:nrow(InputMatrix),3000)
InputMatrix_sub <- InputMatrix[seed_idx,]
object <- CreateIRISFGMObject(InputMatrix_sub)

## ----add_metadata, eval= TRUE, echo = TRUE------------------------------------
my_meta <- read.table(url("https://raw.githubusercontent.com/BMEngineeR/IRISFGM-data/main/Data/Yan_cell_label.txt"),header = TRUE,row.names = 1)
object <- AddMeta(object, meta.info = my_meta)

## ----plot_metadata,eval= TRUE, echo = TRUE------------------------------------
PlotMeta(object)

## ----subset_data,eval= TRUE, echo =  TRUE-------------------------------------
object <- SubsetData(object , nFeature.upper=2000,nFeature.lower=250)

## ----ProcessData,echo = TRUE, eval= TRUE--------------------------------------
object <- ProcessData(object, normalization = "cpm", IsImputation = FALSE)

## ----run_LTMG, echo = TRUE,eval = TRUE----------------------------------------
# do not show progress bar
quiet <- function(x) { 
  sink(tempfile()) 
  on.exit(sink()) 
  invisible(force(x)) 
} 
# demo only run top 500 gene for saving time.
object <- quiet(RunLTMG(object, Gene_use = "500"))
# you can get LTMG signal matrix
LTMG_Matrix <- GetLTMGmatrix(object)
LTMG_Matrix[1:5,1:5]

## ----biclustering_basedLTMG,eval= TRUE,echo = TRUE----------------------------
object <- CalBinaryMultiSignal(object)
# Please uncomment the following command and make sure to set a correct working directory so that the following command will generate intermeidate files.
# object <- RunBicluster(object, DiscretizationModel = "LTMG",OpenDual = FALSE,
#                        NumBlockOutput = 100, BlockOverlap = 0.5, BlockCellMin = 25)


## ----Run_dimReduce, eval= TRUE, echo = TRUE-----------------------------------
# demo only run top 500 gene for saving time.
object <- RunDimensionReduction(object, mat.source = "UMImatrix",reduction = "umap")
object <- RunClassification(object, k.param = 20, resolution = 0.8, algorithm = 1)

## ----cell_type, eval=TRUE, echo =TRUE-----------------------------------------
# Please uncomment the following command and make sure your working directory is the same as the directory containing intermediate output files. 
# object <- FindClassBasedOnMC(object)

## ----load_example_object, eval= TRUE, echo = TRUE-----------------------------
data("example_object")
getMeta(example_object)[1:5,]

## ----bicluster_network, eval=TRUE, echo =TRUE---------------------------------
PlotNetwork(example_object,N.bicluster = c(1:20))

## ----bicluster_heatmap, eval=TRUE, echo =TRUE---------------------------------
PlotHeatmap(example_object,N.bicluster = c(1, 20),show.clusters = TRUE,show.annotation=TRUE)

## ----bicluster_network_module, eval=TRUE, echo =TRUE--------------------------
PlotModuleNetwork(example_object,N.bicluster = 3,method = "spearman",
                  cutoff.neg = -0.5,
                  cutoff.pos = 0.5,
                  layout = "circle",
                  node.label = TRUE,
                  node.col = "black",
                  node.label.cex = 10)


## ----cell_clustering_umap, eval=TRUE, echo =TRUE------------------------------
# cell clustering results based on Seurat clustering method 
PlotDimension(example_object,  reduction = "umap",idents = "Seurat_r_0.8_k_20")
# cell clustering results based on MCL clustering method 
PlotDimension(example_object, reduction = "umap",idents = "MC_Label")

## ----cell_clustering_globalmarker, eval=TRUE, echo =TRUE----------------------
global_marker <- FindGlobalMarkers(example_object,idents = "Seurat_r_0.8_k_20")
PlotMarkerHeatmap(Globalmarkers = global_marker,object = example_object,idents ="Seurat_r_0.8_k_20")

## -----------------------------------------------------------------------------
sessionInfo()

