pheatmap: Error in col[as.numeric(cut(x, breaks = breaks, include.lowest = T))] : object of type 'closure' is not subsettable

Asked Nov 07 '17 at 11:12

Active Oct 08 '20 at 21:46

Viewed 861 times

I am trying to generate a heatmap with the pheatmap package, however, I keep coming up against various issues (I am new to R). The code I am using is:

  pheatmap(
  mat               = newdata,
  color             = colorRampPalette,
  border_color      = NA,
  show_colnames     = FALSE,
  show_rownames     = FALSE,
  annotation_col    = ColumnLabelsValue,
  annotation_row    = RowLabelsValue,
  annotation_colors = NA,
  drop_levels       = TRUE,
  fontsize          = 10,
  main              = "Default Heatmap")

My data is all numeric and I have removed all NA values, but I am now getting this error.

Error in col[as.numeric(cut(x, breaks = breaks, include.lowest = T))] : object of type 'closure' is not subsettable

Can anyone suggest any resolutions?

edited Oct 08 '20 at 21:46

Werner Hertzog

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asked Nov 07 '17 at 11:12

Leeanne McCarthy

I believe `color` must be a vector, while `colorRampPalette` is a function returning a function. – Stéphane Laurent Nov 07 '17 at 12:03
Thank you for that, it appears to have resolved that problem. I am now getting this error. Error in grid.pretty(range(as.vector(breaks))) : infinite axis extents [GEPretty(nan,nan,5)]. Do you have any ideas? – Leeanne McCarthy Nov 07 '17 at 12:19
1

No idea, sorry. – Stéphane Laurent Nov 07 '17 at 12:20

pheatmap: Error in col[as.numeric(cut(x, breaks = breaks, include.lowest = T))] : object of type 'closure' is not subsettable

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