I need to make a heatmap for RNA expression in different types of cancer. I would like to do it with circlize, and divide my circle in 5 parts (each part is one type of cancer).
I couldn't figure out how to input the data and make the circle divided accordingly.
Is there a way to connect the heatmaps made with Complexheatmap and turn them into circles? For instance, I created my heatmaps like this:
mat <- read.csv("C:/Users/xxxxxxxxx", header=TRUE) #bring csv file
rownames(mat) <- mat [, 1] #First row is label (Genes names)
mat1 <- mat[,colnames(mat)!="Genes"] #delete the Genes names column because it was appearing as part of heatmap
mat2 <- data.matrix(mat1) # transform dataframe to matrix
Heatmap(mat2) #make the heatmap from mat Complexheat map package
col_fun = colorRamp2(c(-20, 0, 20), c("green", "white", "red")) #set the colors and grading
col_fun (seq(-5, 5))
Heatmap(mat2, name = "mat2",
row_order = order(as.numeric(gsub("row", "", rownames(mat2)))),
column_order = order(as.numeric(gsub("column", "", colnames(mat2)))),
column_title = "Head and Neck", col = col_fun) #new heatmap with colors and grading, and organized by order of genes
#MAKE A LIST OF HEATMAPS TOGETHER
ht1 = Heatmap(data2, name = "data2",
row_order = order(as.numeric(gsub("row", "", rownames(data2)))),
column_order = order(as.numeric(gsub("column", "", colnames(data2)))),
column_title = "Soft Tissue", col = col_fun)
ht2 = Heatmap(mat2, name = "mat2",
row_order = order(as.numeric(gsub("row", "", rownames(mat2)))),
column_order = order(as.numeric(gsub("column", "", colnames(mat2)))),
column_title = "Head and Neck", col = col_fun)
ht3 = Heatmap(ov2, name = "ov2",
row_order = order(as.numeric(gsub("row", "", rownames(ov2)))),
column_order = order(as.numeric(gsub("column", "", colnames(ov2)))),
column_title = "Ovary/Fallopian tube", col = col_fun)
ht4 = Heatmap(br3, name = "br3",
row_order = order(as.numeric(gsub("row", "", rownames(br3)))),
column_order = order(as.numeric(gsub("column", "", colnames(br3)))),
column_title = "Breast", col = col_fun)
ht5 = Heatmap(ot2, name = "ot2",
row_order = order(as.numeric(gsub("row", "", rownames(ot2)))),
column_order = order(as.numeric(gsub("column", "", colnames(ot2)))),
column_title = "Other", col = col_fun)
ht_list = ht1 + ht2 + ht3 + ht4 + ht5 #put all together
draw(ht_list, ht_gap = unit(1, "cm")) #adjust the separation size between each heatmap
With this code I could generate the plain form of the heatmap, separated by each cancer type. Is it possible to now turn this heatmap into a circle, keeping the divison?
I tried to use the tutorial made by Zuguang Gu. But since I am still learning R, I am already stuck in the beginning since he makes the tutorial from an automatically generated matrix, and everything develops from it, so I can't figure out how to make the split in a matrix that is inputted from the data I already have.
