Error while using ComplexHeatmap
1
1
Entering edit mode
19 months ago

Hi,

I am using the ComplexHeatmap library to obtain the heatmap of the data. There are 19 rows (samples- different timepoints) and 264 genes (columns). There are few missing values in the data frame. I keep getting the below error message. Also attached is the screenshot of the data. Please assist me in resolving this error.

library(ComplexHeatmap)
library(circlize)

Neg_Dct <- read.csv(file = "./NegDCt_Subject_B1.csv",stringsAsFactors = FALSE)

## Check missing values ##
is.na(Neg_Dct)

## Create a data frame by ignoring columns 1 to 4- categorical data###
df = Neg_Dct[,-c(1:4)]

my_matrix <- as.matrix(df)

class(df)
[1] "data.frame"
class(my_matrix)
[1] "matrix"

Heatmap(my_matrix)

Error in hclust(get_dist(t(mat), distance), method = method) : 
  NA/NaN/Inf in foreign function call (arg 11)

Imgur

ComplexHeatmap missing values R library • 383 views
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3
Entering edit mode
19 months ago
russhh 5.5k

The NAs in your data are causing the clustering to fail. If you want clustering, you could either restrict to complete cases or do the clustering over imputed values; then I think you can pass in the cluster object to ComplexHeatmap (Can't quite remember TBH)

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0
Entering edit mode

Thank you very much @russhh.

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