stage_heatmap

library(ComplexHeatmap)

## Loading required package: grid

## ========================================
## ComplexHeatmap version 2.18.0
## Bioconductor page: http://bioconductor.org/packages/ComplexHeatmap/
## Github page: https://github.com/jokergoo/ComplexHeatmap
## Documentation: http://jokergoo.github.io/ComplexHeatmap-reference
## 
## If you use it in published research, please cite either one:
## - Gu, Z. Complex Heatmap Visualization. iMeta 2022.
## - Gu, Z. Complex heatmaps reveal patterns and correlations in multidimensional 
##     genomic data. Bioinformatics 2016.
## 
## 
## The new InteractiveComplexHeatmap package can directly export static 
## complex heatmaps into an interactive Shiny app with zero effort. Have a try!
## 
## This message can be suppressed by:
##   suppressPackageStartupMessages(library(ComplexHeatmap))
## ========================================

remove_adeno <- readRDS("~/Documents/r_codes/remove_adeno.rds")
filtered_df <- remove_adeno[,-1]
filtered_matrix <- as.matrix(filtered_df)
filtered_matrix[filtered_matrix < 0.05] <- 0
filtered_matrix[filtered_matrix >= 0.05 & filtered_matrix < 0.15] <- 0.1
filtered_matrix[filtered_matrix >= 0.15 & filtered_matrix < 0.25] <- 0.2
filtered_matrix[filtered_matrix >= 0.25 & filtered_matrix < 0.35] <- 0.3
filtered_matrix[filtered_matrix >= 0.35 & filtered_matrix < 0.45] <- 0.4
filtered_matrix[filtered_matrix >= 0.45 & filtered_matrix < 0.55] <- 0.5
filtered <- t(filtered_matrix)
heatmap <- Heatmap(filtered,
                    column_split = list(remove_adeno$merged_stage),
                    cluster_column = TRUE,
                    cluster_rows = FALSE,
                    show_row_names = TRUE,
                    row_title_rot = 90,
                    column_names_rot = 360,
                    show_column_names = FALSE,
                    cluster_column_slices = FALSE,
                    row_title = "adeno heatmap"
)
                   
draw(heatmap)

library(ComplexHeatmap)
remove_scc <- readRDS("~/Documents/r_codes/remove_scc.rds")
filtered_df <- remove_scc[,-1]
filtered_matrix <- as.matrix(filtered_df)
filtered_matrix[filtered_matrix < 0.05] <- 0
filtered_matrix[filtered_matrix >= 0.05 & filtered_matrix < 0.15] <- 0.1
filtered_matrix[filtered_matrix >= 0.15 & filtered_matrix < 0.25] <- 0.2
filtered_matrix[filtered_matrix >= 0.25 & filtered_matrix < 0.35] <- 0.3
filtered_matrix[filtered_matrix >= 0.35 & filtered_matrix < 0.45] <- 0.4
filtered_matrix[filtered_matrix >= 0.45 & filtered_matrix < 0.55] <- 0.5
filtered <- t(filtered_matrix)
heatmap <- Heatmap(filtered,
                    column_split = list(remove_scc$merged_stage),
                    cluster_column = TRUE,
                    cluster_rows = FALSE,
                    show_row_names = TRUE,
                    row_title_rot = 90,
                    column_names_rot = 360,
                    show_column_names = FALSE,
                    cluster_column_slices = FALSE,
                    row_title = "scc heatmap"
)
                   
draw(heatmap)

library(ComplexHeatmap)
remove_adeno_selected <- readRDS("~/Documents/r_codes/remove_adeno_selected.rds")
filtered_df <- remove_adeno_selected[,-7]
filtered_matrix <- as.matrix(filtered_df)
filtered_matrix[filtered_matrix < 0.05] <- 0
filtered_matrix[filtered_matrix >= 0.05 & filtered_matrix < 0.15] <- 0.1
filtered_matrix[filtered_matrix >= 0.15 & filtered_matrix < 0.25] <- 0.2
filtered_matrix[filtered_matrix >= 0.25 & filtered_matrix < 0.35] <- 0.3
filtered_matrix[filtered_matrix >= 0.35 & filtered_matrix < 0.45] <- 0.4
filtered_matrix[filtered_matrix >= 0.45 & filtered_matrix < 0.55] <- 0.5
filtered <- t(filtered_matrix)
heatmap <- Heatmap(filtered,
                    column_split = list(remove_adeno_selected$merged_stage),
                    cluster_column = TRUE,
                    cluster_rows = FALSE,
                    show_row_names = TRUE,
                    row_title_rot = 90,
                    column_names_rot = 360,
                    show_column_names = FALSE,
                    cluster_column_slices = FALSE,
                   row_title = "Adeno selected"
)
                   
draw(heatmap)

library(ComplexHeatmap)
remove_sq_selected <- readRDS("~/Documents/r_codes/remove_sq_selected.rds")
filtered_df <- remove_sq_selected[,-5]
filtered_matrix <- as.matrix(filtered_df)
filtered_matrix[filtered_matrix < 0.05] <- 0
filtered_matrix[filtered_matrix >= 0.05 & filtered_matrix < 0.15] <- 0.1
filtered_matrix[filtered_matrix >= 0.15 & filtered_matrix < 0.25] <- 0.2
filtered_matrix[filtered_matrix >= 0.25 & filtered_matrix < 0.35] <- 0.3
filtered_matrix[filtered_matrix >= 0.35 & filtered_matrix < 0.45] <- 0.4
filtered_matrix[filtered_matrix >= 0.45 & filtered_matrix < 0.55] <- 0.5
filtered <- t(filtered_matrix)
heatmap <- Heatmap(filtered,
                    column_split = list(remove_sq_selected$merged_stage),
                    cluster_column = TRUE,
                    cluster_rows = FALSE,
                    show_row_names = TRUE,
                    row_title_rot = 90,
                    column_names_rot = 360,
                    show_column_names = FALSE,
                    cluster_column_slices = FALSE,
                   row_title = "scc selected"
)
                   
draw(heatmap)