Gene mutation Circular Plot

Getting Started

In genetics, the mutation rate is the frequency of new mutations in a single gene or organism over time.Mutation rates are not constant and are not limited to a single type of mutation;there are many different types of mutations. Mutation rates are given for specific classesof mutations. Point mutations are a class of mutations which are changes to a single base.Missense and Nonsense mutations are two subtypes of point mutations. The rate of these types of substitutionscan be further subdivided into a mutation spectrum which describes the influence of the genetic context on the mutation rate

Installation and load R libraries

### Step_1 Downloading R pakchaes

 if (!requireNamespace("BiocManager", quietly = TRUE))
 install.packages("BiocManager")

 BiocManager::install(c("ggplot2", "pacman", " plotrix", "DMRcate", " circlize", " dplyr"))

 ### Step_2 Loading libraries

library(ggplot2)
library(plotrix)
library(circlize)
library(pacman)

Creating seperate category for each gene percentage of mutations

    ### Step_1 Creat a list of genes 
    category <- c("HGNC", "ADCY5", "APOC3", "BCL2","CDKN1A", "CTF1", "EGR1", "FEN1", "GDF11")

    ### Step_2 Creat a list of pecentae of mutations
    percent <- c(75, 65, 45, 69, 35, 44, 62, 80, 50)

Creating Circular polot for pcentae of mutation pe gene

 color= c("#7C0A02", "#FAE7B5", "#7C0A02", "#FAE7B5", "#7C0A02", "#FAE7B5", "#7C0A02", "#FAE7B5", "#7C0A02")


 circos.par("start.degree" = 90, cell.padding = c(0, 0, 0, 0))
 circos.initialize("a", xlim = c(0, 100)) # 'a` just means there is one sector
 circos.track(ylim = c(0.5, length(percent)+0.5), track.height = 0.8, 
         bg.border = NA, panel.fun = function(x, y) {
           xlim = CELL_META$xlim
           circos.segments(rep(xlim[1], 9), 1:9,
                           rep(xlim[2], 9), 1:9,
                           col = "#CCCCCC")
           circos.rect(rep(0, 9), 1:9 - 0.45, percent, 1:9 + 0.45,
                       col = color, border = "white")
           circos.text(rep(xlim[1], 9), 1:9, 
                       paste(category, " - ", percent, "%"), 
                       facing = "downward", adj = c(1.05, 0.5), cex = 0.8) 
           breaks = seq(0, 85, by = 5)
           circos.axis(h = "top", major.at = breaks, labels = paste0(breaks, "%"), 
                       labels.cex = 0.6)
         })



   circos.clear()

  dev.off()