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)
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?
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