library(dplyr)
library(tidyr)
library(ggplot2)
library(ComplexHeatmap)


setwd("C:/Users/forey/Downloads/limma_on_data_20_and_data_27__Report")
ForHeatmap <- read.delim("C:/Users/forey/Downloads/limma_on_data_20_and_data_27__Report/ForHeatmap.txt")

Tablem <- as.matrix(ForHeatmap[,2:4])
rownames(Tablem) = paste0(ForHeatmap$Name)

TablemH1 = Heatmap(Tablem, name = "m",
                   column_title = "Conditions",
                   column_title_side = "bottom",
                   column_title_gp = gpar(fontsize = 2, fontface = "bold"),
                   row_title = "Genes",
                   row_title_side = "right",
                   row_title_gp = gpar(fontsize = 2, fontface = "bold"),
                   row_title_rot = 0,
                   cluster_rows = TRUE,
                   cluster_columns = FALSE,
                   show_column_dend = TRUE,
                   show_row_dend = FALSE,
                   show_row_names = TRUE,
                   show_column_names = TRUE,
                   #clustering_distance_rows = "pearson",
                   column_km = 1,
                   row_km = 3)
draw(TablemH1) #Unscaled


ForHeatmapCount <- read.delim("C:/Users/forey/Downloads/limma_on_data_20_and_data_27__Report/ForHeatmapCount.txt")
Tablem <- as.matrix(ForHeatmapCount[,2:13])
rownames(Tablem) = paste0(ForHeatmapCount$Name)

Tablem <- t(Tablem)
Tablem <- scale(Tablem)
Tablem <- t(Tablem)

TablemH1 = Heatmap(Tablem, name = "m",
                   column_title = "Conditions",
                   column_title_side = "bottom",
                   column_title_gp = gpar(fontsize = 2, fontface = "bold"),
                   row_title = "Genes",
                   row_title_side = "right",
                   row_title_gp = gpar(fontsize = 2, fontface = "bold"),
                   row_title_rot = 0,
                   cluster_rows = TRUE,
                   cluster_columns = FALSE,
                   show_column_dend = TRUE,
                   show_row_dend = TRUE,
                   show_row_names = TRUE,
                   show_column_names = FALSE,
                   #clustering_distance_rows = "pearson",
                   column_km = 1,
                   row_km = 1)
draw(TablemH1) #Unscaled

Violin <- read.delim("C:/Users/forey/Downloads/limma_on_data_20_and_data_27__Report/Violin.txt")
ggplot(Violin, aes(x=Condition, y=Score)) +
geom_violin(trim=FALSE, fill='#A4A4A4', color="darkred")+
geom_boxplot(width=0.1) + theme_minimal()
