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plot(cars)

NA
NA

install.packages("circlize")

Error in install.packages : Updating loaded packages

library(circlize)
mat = matrix(sample(1:100, 18, replace = TRUE), 3, 6)
rownames(mat) = letters[1:3]
colnames(mat) = LETTERS[1:6]
par(cex = 2, mar = c(0, 0, 0, 0))
chordDiagram(mat)

install.packages("readxl")

Error in install.packages : Updating loaded packages

library(readxl)

# Specify sheet with a number or name
figure_5_A <- read_excel("Table_5.xlsx", sheet = "Fig5 panel a")

print(theData)

chordDiagram(theData)

figure_5_B <- read_excel("Table_5.xlsx", sheet = "Fig 5 panel b")

figure_5_B

library(gridExtra)
chordDiagram(figure_5_B, grid.col = grid.col, annotationTrack = "grid", cl = "table")

Error in chordDiagramFromDataFrame(x, grid.col = grid.col, grid.border = grid.border,  : 
  object 'grid.col' not found

layout(matrix(1:9, 3, 3))
for(i in 1:9) {
    sectors = 1:8
    par(mar = c(0.5, 0.5, 0.5, 0.5))
    circos.par(cell.padding = c(0, 0, 0, 0))
    circos.initialize(sectors, xlim = c(0, 1))
    circos.track(ylim = c(0, 1), track.height = 0.05,
        bg.col = rand_color(8), bg.border = NA)
    for(i in 1:20) {
        se = sample(1:8, 2)
        circos.link(se[1], runif(2), se[2], runif(2), 
            col = rand_color(1, transparency = 0.4), border = NA)
    }
    circos.clear()
}

circos.initializeCircularGenome(figure_5_B)

Error in data.frame(name, 0, genome_size) : 
  argument "genome_size" is missing, with no default

{rcos.par(cell.padding = c(0, 0, 0, 0))} circos.initialize(sectors, xlim = c(0, 1)) circos.track(ylim = c(0, 1), track.height = 0.05, bg.col = rand_color(8), bg.border = NA) for(i in 1:20) { se = sample(1:8, 2) circos.link(se[1], runif(2), se[2], runif(2), col = rand_color(1, transparency = 0.4), border = NA) } circos.clear() }

{chordDiagram(figure_5_B, grid.col = grid.col, annota}

df <-figure_5_B[order(-figure_5_B$"Number of shared GCFs"),]
head(df)

df <-figure_5_B[order(-figure_5_B$"Number of shared GCFs"),]
head(df)

df2 <-figure_5_A[order(figure_5_A$"Number of shared GCFs"),]
head(df2)