add_build_orthg_db_tutorial

README.Rmd

@@ -54,7 +54,9 @@ For users who want to perform cross-species analysis quickly, we provide a brief
 
 [Quick tutorial for identifying evolutionally conserved gene regulatory networks](https://jiang-junyao.github.io/CACIMAR/quick_grn.html)
 
-[Quick tutorial for identifying evolutionally conserved ligand-receptor interaction and cell-cell communications (coming soon)]()
+[Quick tutorial for identifying evolutionally conserved ligand-receptor interaction and cell-cell communications](https://jiang-junyao.github.io/CACIMAR/quick_interaction.html)
+
+[Tutorial for build customized orthg database based on MGI](https://jiang-junyao.github.io/CACIMAR/build_db.html)
 
 ## Examples
 

README.md

@@ -49,7 +49,11 @@ data](https://jiang-junyao.github.io/CACIMAR/quick_celltype.html)
 networks](https://jiang-junyao.github.io/CACIMAR/quick_grn.html)
 
 [Quick tutorial for identifying evolutionally conserved ligand-receptor
-interaction and cell-cell communications (coming soon)]()
+interaction and cell-cell
+communications](https://jiang-junyao.github.io/CACIMAR/quick_interaction.html)
+
+[Tutorial for build customized orthg database based on
+MGI](https://jiang-junyao.github.io/CACIMAR/build_db.html)
 
 ## Examples
 

docs/.Rhistory

@@ -0,0 +1,54 @@
+## Global options
+knitr::opts_chunk$set(cache = TRUE)
+library(CACIMAR)
+load(system.file("extdata", "zf_mm_markers.rda", package = "CACIMAR"))
+### identify evolutionarily conserved cell types based on conservation score of cell types (CSCT)
+OrthG <- OrthG_Mm_Zf
+expression <- Identify_ConservedCellTypes(OrthG, Zf_marker, Mm_marker,'zf','mm')
+### identify evolutionarily conserved cell types based on conservation score of cell types (CSCT)
+OrthG <- OrthG_Mm_Zf
+expression <- Identify_ConservedCellTypes(OrthG, zf_marker, mm_marker,'zf','mm')
+SCT_matrix <- expression[[2]]
+SNT_h <- SNT[grep('mm',rownames(SCT_matrix)),as.numeric(grep('zf',colnames(SCT_matrix)))]
+SNT_h <- expression[[2]][grep('mm',rownames(SCT_matrix)),as.numeric(grep('zf',colnames(SCT_matrix)))]
+Heatmap_Cor(SNT_h,cluster_cols=F, cluster_rows=F,Color1 = c(rgb(102/255,46/255,115/255),rgb(31/255,153/255,139/255),rgb(251/255,232/255,48/255)))
+Heatmap_Cor(expression[[2]],cluster_cols=F, cluster_rows=F,Color1 = c(rgb(102/255,46/255,115/255),rgb(31/255,153/255,139/255),rgb(251/255,232/255,48/255)))
+Heatmap_Cor(SNT_h,cluster_cols=T, cluster_rows=T,Color1 = c(rgb(102/255,46/255,115/255),rgb(31/255,153/255,139/255),rgb(251/255,232/255,48/255)))
+### get the conserved cell types based on the mutually matched and bigger than 3/4 CSCT score
+conserved_hm_celltypes <- get_conserved_hm_celltypes(SNT_h)
+get_conserved_hm_celltypes <- function(data) {
+conserved_hm_celltypes_df <- data.frame()
+for (i in 1:nrow(data)) {
+single_row <- data[i, ]
+max_col_id <- which.max(single_row)
+single_col <- data[, max_col_id]
+max_row_id <- which.max(single_col)
+if (max_row_id == i) {
+if (data[i, max_col_id] > quantile(data, 0.75)) {
+conserved_hm_celltypes_df <- rbind(conserved_hm_celltypes_df, c(rownames(data)[i], colnames(data)[max_col_id]))
+}
+}
+}
+conserved_hm_celltypes <- unlist(as.vector(conserved_hm_celltypes_df), use.names = FALSE)
+return(conserved_hm_celltypes)
+}
+### get the conserved cell types based on the mutually matched and bigger than 3/4 CSCT score
+conserved_hm_celltypes <- get_conserved_hm_celltypes(SNT_h)
+### used my pointed colors
+load(system.file("extdata", "zf_mm_colors_prefix.Rda", package = "CACIMAR"))
+### generate a phylogenetic tree
+p <- Plot_phylogenetic_tree(SCT_matrix = SCT_matrix,
+species.vector = species.vector,
+conserved_hm_celltype = conserved_hm_celltypes,
+annotation_colors_df = bind_colors,
+colors_labels = c("Mouse", "Zebrafish"))
+View(mm_marker)
+mm_marker$cluster
+mm_marker$cluster = gsub('mm','',mm_marker$cluster)
+zf_marker$cluster = gsub('zf','',zf_marker$cluster)
+SCT_matrix <- expression[[2]]
+SNT_h <- expression[[2]][grep('mm',rownames(SCT_matrix)),as.numeric(grep('zf',colnames(SCT_matrix)))]
+### show the CSCT value with a heatmap
+Heatmap_Cor(SNT_h,cluster_cols=F, cluster_rows=F,Color1 = c(rgb(102/255,46/255,115/255),rgb(31/255,153/255,139/255),rgb(251/255,232/255,48/255)))
+save(mm_marker,zf_marker,'F:\\platform\\CCtMR\\inst\\extdata\\zf_mm_markers.rda')
+save(mm_marker,zf_marker,file = 'F:\\platform\\CCtMR\\inst\\extdata\\zf_mm_markers.rda')