Entering edit mode
4.1 years ago
ngcatung0
▴
20
Hi,
I keep getting this error and have no idea how to get past it. The error is:
Error in Heatmap(my_matrix, cluster_columns = FALSE, row_names_side = "left", :
unused argument (row_hclust_side = "left")
Please help! Below is the script until I received the error.
Thank you!!
library(ComplexHeatmap)
setwd("\\Users\\catungng\\Desktop\\Practice")
#Select a data file
filename <- ".txt"
# Read the data into a data.frame
my_data <- read.table("alterations_across_samples.tsv", sep="\t", quote="", stringsAsFactors=FALSE,header=TRUE)
head(my_data)
dim(my_data) # (rows columns)
nrow(my_data) # rows: locations (bins) in genome
ncol(my_data) # columns: cells
# Make the heatmap data into a matrix
my_matrix <- as.matrix(my_data[ ,c(4:100)]) # [all rows, columns 4-100]
# leave out the first 3 columns (chrom,start,end) since they don't belong in the heatmap itself
# We can check the classes:
class(my_data)
class(my_matrix)
head(my_matrix)
# Save chromosome column for annotating the heatmap later
chromosome_info <- data.frame(chrom = my_data$CHR)
chromosome_info
## Now we make our first heatmap
# Default parameters
Heatmap(my_matrix)
# Flip rows and columns around
my_matrix <- t(my_matrix) # "transpose"
Heatmap(my_matrix)
# Keep genome bins in order, not clustered
Heatmap(my_matrix, cluster_columns=FALSE)
fontsize <- 0.6
# Put cell labels on the left side
Heatmap(my_matrix, cluster_columns=FALSE,
row_names_side = "left",
row_hclust_side = "left",
row_names_gp=gpar(cex=fontsize))