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barplot_of_clusters.R
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barplot_of_clusters.R
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# get bar plots of cluster assignment
# Load required libraries
library(reshape2)
library(ggplot2)
library(ggpubr)
library(RColorBrewer)
# Clear the workspace
rm(list=ls())
# read data
cluster_results <- readRDS("../results/euler_memberships.rds")
mutation_covariate_data <- readRDS("../data/aml_data.rds")
table(cluster_results$clustermembership)
k_clust <- length(levels(as.factor(cluster_results$clustermembership)))
cancer_table <- matrix(NA, k_clust, 4)
colnames(cancer_table) <- c("AML", "MDS", "MPN", "CMML")
rownames(cancer_table) <- LETTERS[1:k_clust]
for (ii in 1:k_clust){
count_aml <- length(which(mutation_covariate_data$Dx[which(cluster_results$clustermembership==ii)]=="AML"))
count_mds <- length(which(mutation_covariate_data$Dx[which(cluster_results$clustermembership==ii)]=="MDS"))
count_mpn <- length(which(mutation_covariate_data$Dx[which(cluster_results$clustermembership==ii)]=="MPN"))
count_cmml <- length(which(mutation_covariate_data$Dx[which(cluster_results$clustermembership==ii)]=="CMML"))
cancer_table[ii,] <- c(count_aml, count_mds, count_mpn, count_cmml)
}
mycolor <- c("#DD7788", "#771122", "#DDDD77", "#117777")
p2 <- ggbarplot(melt(cancer_table), "Var1", "value",
fill = "Var2", color = "Var2", palette = mycolor,
label = TRUE, lab.col = NA)+
# label = TRUE, lab.col = "white", lab.pos = "in")+
xlab("Clusters") +
# ylab("Number of Patients") +
ylab("Patients per cluster") +
guides(fill=guide_legend(title="Cancer Type"),col = FALSE)+
theme(legend.position="off",
axis.line=element_blank(),
axis.text.y=element_blank(), #remove y axis labels
axis.ticks.y=element_blank(),
axis.ticks.x=element_blank()); p2
# save plot
saveRDS(p2, "../figures/barplot.rds")
p22 <- ggbarplot(melt(cancer_table), "Var1", "value",
fill = "Var2", color = "Var2", palette = mycolor,
label = TRUE, lab.col = NA)+
# label = TRUE, lab.col = "white", lab.pos = "in")+
xlab("Clusters") +
# ylab("Number of Patients") +
ylab("") +
guides(fill=guide_legend(title="Cancer type"),col = FALSE)+
theme(legend.position="bottom",
axis.line=element_blank(),
axis.text.y=element_blank(), #remove y axis labels
axis.ticks.y=element_blank(),
axis.ticks.x=element_blank()); p22
cluster_legend <- get_legend(p22)
# save legend
saveRDS(cluster_legend, "../figures/bar_legend_ct.rds")
# df_cancer_table <- melt(cancer_table)
#
# df_cancer_table$Var1 <- factor(df_cancer_table$Var1, # Change ordering manually
# levels = c("A","H","F","I","C","E","D","B","G"))
#
# p2 <- ggbarplot(df_cancer_table, "Var1", "value",
# fill = "Var2", color = "Var2", palette = mycolor,
# label = TRUE, lab.col = NA)+
# # label = TRUE, lab.col = "white", lab.pos = "in")+
# xlab("Clusters") +
# # ylab("Number of Patients") +
# ylab("") +
# guides(fill=guide_legend(title="Cancer Type"),col = FALSE)+
# theme(legend.position="off",
# axis.line=element_blank(),
# axis.text.y=element_blank(), #remove y axis labels
# axis.ticks.y=element_blank(),
# axis.ticks.x=element_blank()); p2
#
# # save plot
# saveRDS(p2, "../figures/barplot.rds")