rdata-visualizationcirclize

circos.heatmap(): Error in rowMeans(m) : 'x' must be an array of at least two dimensions


I'm following the tutorial to make circular plots in R. Suppose I have this dataset:

set.seed(123)
    mat1 = rbind(cbind(matrix(rnorm(50*5, mean = 1), nr = 50), 
                   matrix(rnorm(50*5, mean = -1), nr = 50)),
                cbind(matrix(rnorm(50*5, mean = -1), nr = 50), 
                   matrix(rnorm(50*5, mean = 1), nr = 50))
                )
    rownames(mat1) = paste0("R", 1:100)
    colnames(mat1) = paste0("C", 1:10)
    mat1 = mat1[sample(100, 100), ] # randomly permute rows
    split = sample(letters[1:5], 100, replace = TRUE)
    split = factor(split, levels = letters[1:5])

I tried using Heatmap and it returns appropriately.

library(ComplexHeatmap)
Heatmap(mat1, row_split = split)

enter image description here

However, when I try to use circos.heatmap(), it returns error:

library(circlize)
col_fun1 = colorRamp2(c(-2, 0, 2), c("blue", "white", "red"))
circos.heatmap(mat = mat1, split = split, col = col_fun1)
circos.heatmap(mat = mat1, col = col_fun1)
> Error in rowMeans(m) : 'x' must be an array of at least two dimensions

The matrix itself has a dimension of 100 x 10. Is there anything I'm missing?


Solution

  • Had the same issue with CRAN version, but it was rectified after installing the dev version

    devtools::install_github("jokergoo/circlize")
    

    -testing

    > library(circlize)
    ========================================
    circlize version 0.4.13
    CRAN page: https://cran.r-project.org/package=circlize
    Github page: https://github.com/jokergoo/circlize
    Documentation: https://jokergoo.github.io/circlize_book/book/
    
    If you use it in published research, please cite:
    Gu, Z. circlize implements and enhances circular visualization
      in R. Bioinformatics 2014.
    
    This message can be suppressed by:
      suppressPackageStartupMessages(library(circlize))
    ========================================
    
    > col_fun1 = colorRamp2(c(-2, 0, 2), c("blue", "white", "red"))
    > ?circos.heatmap
    starting httpd help server ... done
    > 
    > set.seed(123)
    > mat1 = rbind(cbind(matrix(rnorm(50*5, mean = 1), nr = 50), 
    +                    matrix(rnorm(50*5, mean = -1), nr = 50)),
    +              cbind(matrix(rnorm(50*5, mean = -1), nr = 50), 
    +                    matrix(rnorm(50*5, mean = 1), nr = 50))
    +             )
    > rownames(mat1) = paste0("R", 1:100)
    > colnames(mat1) = paste0("C", 1:10)
    > mat1 = mat1[sample(100, 100), ] # randomly permute rows
    > split = sample(letters[1:5], 100, replace = TRUE)
    > spilt = factor(split, levels = letters[1:5])
    > col_fun1 = colorRamp2(c(-2, 0, 2), c("blue", "white", "red"))
    > circos.heatmap(mat1, split = split, col = col_fun1)
    > circos.clear()
    

    -output

    enter image description here