Get Sample Order based on Proliferation Score.

Return a sample order based on the late/early ratio (proliferation score).

Usage

get_sample_order(expr_data = NULL, return_this = "sample_order")

Arguments

expr_data

Required parameter, should be the output from classify_samples(). Note, this function required the classify_samples to be run with include_data = TRUE argument.

return_this

Set to "late_early" to return late/early ratio. Set to "sample_order" to return the sample order based on late/early ratio (default).

Value

Returns the sample order.

Details

Modified version of the heatmap function plot_classification_heatmap(), this function only returns the order of samples to be used for downstream plotting functions. The order is dictated by the early late ratio. and the sample order can readily be sued elsewhere, if needed.

Examples

#run classifier
sjodahl_classes = classify_samples(this_data = sjodahl_2017, 
                                   log_transform = FALSE, 
                                   adjust = TRUE, 
                                   impute = TRUE, 
                                   include_data = TRUE, 
                                   verbose = FALSE)
       
#get sample order                            
get_sample_order(expr_data = sjodahl_classes$data)
#>   [1] 158 194 142 171  43  76 235  83 160  31  68 237 232 187  22 130 259 163
#>  [19] 134 245  55 168 131 234  99  47 161  61 137   7  85 236 199  28 264 175
#>  [37] 254 202 266  13  94 184   3 253 231  26  54 164  95 103 178 179 221 223
#>  [55]  73 224 132 113  46  49 102 166 241 112  97 100  41 167 107 249 239  15
#>  [73] 220  91   9   4 114 242  64  36 119  62 233  56 243  29  98 191 246 225
#>  [91] 247 205  63 222 240 206 227 156  14  79  21 252  58 190  65   1 248 145
#> [109] 117 125 151 200 251 101 155 172 215  51 212 165  78  69  77 162  75  20
#> [127] 218  81 229  24 116 244 126 170 108 105 123  60 141 136 256 133  80 111
#> [145] 138  23  19  48 208  93 159 188  72 216  12 217 192  25 209 147 182   5
#> [163] 181 122 110  18 230  92  27 124  86 135 257 228 152  66  71 183 118  10
#> [181] 204  44  50 121  57  37 250 186  40 197 153 115 219 203  89  30 177  90
#> [199]  96 139 143  42 201 144  11 106  70 176 150 260 154   6 169 238 185 193
#> [217] 207 180  87  33 173  16 149 104 262 195  35 127 258 109 129  59 261  32
#> [235]  52 211 213 148 263  82  38 120   2  45  53  84  74 196 140 174 267 146
#> [253]  39  67 265  88  17 210 255 214 189 226 128   8  34 157 198
#> Returning sample order...
#>   [1] 158 194 142 171  43  76 235  83 160  31  68 237 232 187  22 130 259 163
#>  [19] 134 245  55 168 131 234  99  47 161  61 137   7  85 236 199  28 264 175
#>  [37] 254 202 266  13  94 184   3 253 231  26  54 164  95 103 178 179 221 223
#>  [55]  73 224 132 113  46  49 102 166 241 112  97 100  41 167 107 249 239  15
#>  [73] 220  91   9   4 114 242  64  36 119  62 233  56 243  29  98 191 246 225
#>  [91] 247 205  63 222 240 206 227 156  14  79  21 252  58 190  65   1 248 145
#> [109] 117 125 151 200 251 101 155 172 215  51 212 165  78  69  77 162  75  20
#> [127] 218  81 229  24 116 244 126 170 108 105 123  60 141 136 256 133  80 111
#> [145] 138  23  19  48 208  93 159 188  72 216  12 217 192  25 209 147 182   5
#> [163] 181 122 110  18 230  92  27 124  86 135 257 228 152  66  71 183 118  10
#> [181] 204  44  50 121  57  37 250 186  40 197 153 115 219 203  89  30 177  90
#> [199]  96 139 143  42 201 144  11 106  70 176 150 260 154   6 169 238 185 193
#> [217] 207 180  87  33 173  16 149 104 262 195  35 127 258 109 129  59 261  32
#> [235]  52 211 213 148 263  82  38 120   2  45  53  84  74 196 140 174 267 146
#> [253]  39  67 265  88  17 210 255 214 189 226 128   8  34 157 198