Entering edit mode
I am trying to plot a heatmap using pheatmap().
I'm using the following script to set the parameters and plot the various clusters.
hmx.parameters <- list(counts_filtered_df,
color = col.pal,
cellwidth = 15, cellheight = 12, scale = "none",
treeheight_row = 200,
kmeans_k = 20, # maxclust,
show_rownames = T, show_colnames = T,
main = main,
clustering_method = "average",
cluster_rows = TRUE, cluster_cols = TRUE,
clustering_distance_rows = drows1,
clustering_distance_cols = NA)
# To store cluster mappings and draw
set.seed(123)
kmean.hm <- do.call("pheatmap", hmx.parameters)
But I get the following error
Error in do_one(nmeth) : NA/NaN/Inf in foreign function call (arg 1)
I have read some questions about it and have checked the sd of my matrix. But it seems to be fine
> dim(sample_mat) [1] 2297 100 > counts_filtered<- sample_mat[apply(sample_mat, MARGIN = 1, FUN = function(x) sd(x) != 0),] > dim(counts_filtered) [1] 2297 100
So, even after trying to filter for 0 sd rows, it still does not run.
Is there any other reason for this problem?
thanks, Assa
