comparison heatmap.r @ 53:5a478e171752 draft

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author guerler
date Thu, 05 Jun 2014 13:38:00 -0400
parents eafc7121f553
children 680cf68098d5
comparison
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52:e10dbc437d8f 53:5a478e171752
1 # limits
2 min_limit = 20
3
4 # load sparse matrix package 1 # load sparse matrix package
5 suppressPackageStartupMessages(library('Matrix')) 2 suppressPackageStartupMessages(library('Matrix'))
6 3
7 # access a numeric column 4 # access a numeric column
8 get_numeric <- function(table, column_key) { 5 get_numeric <- function(table, column_key) {
9 column <- as.numeric(column_key) 6 column <- as.numeric(column_key)
10 column_data <- sapply( table[column], as.numeric ) 7 column_data <- suppressWarnings(as.numeric(as.character(table[column][[1]])))
11 return (c(column_data)) 8 return (c(column_data))
12 } 9 }
13 10
14 # access a label column 11 # access a label column
15 get_label <- function(table, column_key) { 12 get_label <- function(table, column_key) {
83 col_order <- hclust(dist(t(my_matrix)))$order 80 col_order <- hclust(dist(t(my_matrix)))$order
84 81
85 # reorder matrix 82 # reorder matrix
86 my_matrix <- my_matrix[row_order, col_order] 83 my_matrix <- my_matrix[row_order, col_order]
87 84
88 # get min size
89 min_limit = max(as.integer(options$limit), min_limit)
90
91 # get max size
92 max_row = min(length(row_order), min_limit)
93 max_col = min(length(col_order), min_limit)
94
95 # transform back to three columns 85 # transform back to three columns
96 my_flatmatrix = flatten(my_matrix[1:max_row, 1:max_col]) 86 my_flatmatrix = flatten(my_matrix)
97 87
98 # append to result list 88 # append to result list
99 l <- append(l, list(my_flatmatrix$i)) 89 l <- append(l, list(my_flatmatrix$i))
100 l <- append(l, list(my_flatmatrix$j)) 90 l <- append(l, list(my_flatmatrix$j))
101 l <- append(l, list(my_flatmatrix$x)) 91 l <- append(l, list(my_flatmatrix$x))