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use number of mutations to sort rows

Zuguang Gu authored on 30/01/2018 10:39:06
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@@ -207,7 +207,7 @@ oncoPrint = function(mat, get_type = function(x) x,
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 	}
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 	oncoprint_row_order = function() {
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-		order(rowSums(count_matrix), pct_num, decreasing = TRUE)
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+		order(rowSums(count_matrix), n_mut, decreasing = TRUE)
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 	}
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 	oncoprint_column_order = function() {
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@@ -225,6 +225,8 @@ oncoPrint = function(mat, get_type = function(x) x,
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 	}
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 	count_matrix = apply(arr, c(1, 2), sum)
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+	n_mut = rowSums(apply(arr, 1:2, any))
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+	
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 	if(is.null(row_order)) row_order = seq_len(nrow(count_matrix))
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 	if(is.null(column_order)) column_order = seq_len(ncol(count_matrix))
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 	row_order = row_order