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DPT
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<code>Input saved to /scratch/irc/personal/robrechtc/tmp//Rtmp8I3Sai/input: <br> data.rds<br> params.json<br>Attaching package: ‘dplyr’<br>The following objects are masked from ‘package:stats’:<br> filter, lag<br>The following objects are masked from ‘package:base’:<br> intersect, setdiff, setequal, union<br>Attaching package: ‘purrr’<br>The following object is masked from ‘package:jsonlite’:<br> flatten<br>Loading required namespace: cellTree<br>Computing LDA model using: VEM<br>Filtering out rows with standard deviation < 0.5 (101 -> 100)...<br>Loading required namespace: topicmodels<br>**** em iteration 10 ****<br>document 92<br>new alpha = 10.05345<br>**** em iteration 20 ****<br>document 92<br>new alpha = 4.00419<br>**** em iteration 30 ****<br>document 92<br>new alpha = 3.89400<br>final e step document 92<br>Model fit for k = 4 topics<br>Using rooting method: longest.path<br>Using root vertex: 79<br>Adding branch #1:<br> [1] 85 81 88 14 7 23 52 25 30 50 28 45 72 77 80 6 20 83 21 86 42 76 62 3 59<br>[26] 56 26 10 87 73 33 18 34 31 66 39 60 5 67 15 68<br>Using branch width: 0.278 (width.scale.factor: 1.5)<br>Outliers: 0<br>Total number of branches: 1 (forks: 0)<br>Backbone fork merge (width: 0.278): 42 -> 42 <br>Ranking all cells...<br>Computing tree layout...output saved in /scratch/irc/personal/robrechtc/tmp//Rtmp8I3Sai/output: <br> output.rds<br></code>
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<code>Input saved to /scratch/irc/personal/robrechtc/tmp//RtmpOUTDeh/input: <br> data.rds<br> params.json<br>Attaching package: ‘dplyr’<br>The following objects are masked from ‘package:stats’:<br> filter, lag<br>The following objects are masked from ‘package:base’:<br> intersect, setdiff, setequal, union<br>Attaching package: ‘purrr’<br>The following object is masked from ‘package:jsonlite’:<br> flatten<br>Loading required namespace: cellTree<br>Computing LDA model using: VEM<br>Filtering out rows with standard deviation < 0.5 (101 -> 101)...<br>Loading required namespace: topicmodels<br>**** em iteration 10 ****<br>document 94<br>new alpha = 2.48084<br>**** em iteration 20 ****<br>document 94<br>new alpha = 2.68166<br>final e step document 94<br>Model fit for k = 4 topics<br>Using rooting method: longest.path<br>Using root vertex: 78<br>Adding branch #1:<br> [1] 17 89 63 5 51 11 39 77 2 54 86 19 68 9 91 10 67 3 72 36 33 6 65 29 49<br>[26] 4 22 71 21 34 60 59 46 92 74 55 27<br>Using branch width: 0.305 (width.scale.factor: 1.5)<br>Outliers: 0<br>Total number of branches: 1 (forks: 0)<br>Backbone fork merge (width: 0.305): 38 -> 38 <br>Ranking all cells...<br>Computing tree layout...output saved in /scratch/irc/personal/robrechtc/tmp//RtmpOUTDeh/output: <br> output.rds<br></code>
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<code>Input saved to /scratch/irc/personal/robrechtc/tmp//RtmpykLWQh/input: <br> data.rds<br> params.json<br>Attaching package: ‘dplyr’<br>The following objects are masked from ‘package:stats’:<br> filter, lag<br>The following objects are masked from ‘package:base’:<br> intersect, setdiff, setequal, union<br>Attaching package: ‘purrr’<br>The following object is masked from ‘package:jsonlite’:<br> flatten<br>Loading required namespace: cellTree<br>Computing LDA model using: VEM<br>Filtering out rows with standard deviation < 0.5 (4480 -> 4480)...<br>Loading required namespace: topicmodels<br>final e step document 238<br>Model fit for k = 4 topics<br>Using rooting method: longest.path<br>Using root vertex: 33<br>Adding branch #1:<br> [1] 7 180 115 228 58 149 87 50 74 231 113 183 171 185 53 218 110 82 205<br>[20] 182 12 234 145 170 101 72 79 60 31 5 14 108 76 157 153 107 137 162<br>[39] 188 23 133 34 146 158<br>Using branch width: 0.22 (width.scale.factor: 1.5)<br>Outliers: 0<br>Total number of branches: 1 (forks: 0)<br>Backbone fork merge (width: 0.22): 45 -> 45 <br>Ranking all cells...<br>Computing tree layout...output saved in /scratch/irc/personal/robrechtc/tmp//RtmpykLWQh/output: <br> output.rds<br></code>
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<code>Input saved to /scratch/irc/personal/robrechtc/tmp//RtmplY0S57/input: <br> data.rds<br> params.json<br>Attaching package: ‘dplyr’<br>The following objects are masked from ‘package:stats’:<br> filter, lag<br>The following objects are masked from ‘package:base’:<br> intersect, setdiff, setequal, union<br>Attaching package: ‘purrr’<br>The following object is masked from ‘package:jsonlite’:<br> flatten<br>Loading required namespace: cellTree<br>Computing LDA model using: VEM<br>Filtering out rows with standard deviation < 0.5 (3379 -> 3379)...<br>Loading required namespace: topicmodels<br>final e step document 355<br>Model fit for k = 4 topics<br>Using rooting method: longest.path<br>Using root vertex: 127<br>Adding branch #1:<br> [1] 68 144 125 96 99 120 85 106 88 92 112 104 137 142 103 26 135 128 115<br>[20] 80 119 72 132 249 15 18 13 308 33 63 178 21 337 289 326 252 168 158<br>[39] 347 237 310 281 229 261 234 327 191 268 349 324 207 224 205 208 221 171 209<br>Using branch width: 0.0576 (width.scale.factor: 1.5)<br>Outliers: 5<br>Total number of branches: 1 (forks: 0)<br>Backbone fork merge (width: 0.0576): 58 -> 58 <br>Ranking all cells...<br>Computing tree layout...output saved in /scratch/irc/personal/robrechtc/tmp//RtmplY0S57/output: <br> output.rds<br></code>
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<code>Input saved to /scratch/irc/personal/robrechtc/tmp//Rtmplk1Rxc/input: <br> data.rds<br> params.json<br>Attaching package: ‘dplyr’<br>The following objects are masked from ‘package:stats’:<br> filter, lag<br>The following objects are masked from ‘package:base’:<br> intersect, setdiff, setequal, union<br>Attaching package: ‘purrr’<br>The following object is masked from ‘package:jsonlite’:<br> flatten<br>Loading required namespace: cellTree<br>Computing LDA model using: VEM<br>Filtering out rows with standard deviation < 0.5 (101 -> 101)...<br>Loading required namespace: topicmodels<br>**** em iteration 10 ****<br>document 95<br>new alpha = 7.68228<br>**** em iteration 20 ****<br>document 95<br>new alpha = 4.24082<br>**** em iteration 30 ****<br>document 95<br>new alpha = 4.18931<br>final e step document 95<br>Model fit for k = 4 topics<br>Using rooting method: longest.path<br>Using root vertex: 48<br>Adding branch #1:<br> [1] 67 95 51 34 40 27 31 71 28 68 47 54 42 15 84 10 93 59 75 86 55 58 61 35 78<br>[26] 4 8 56 39 92<br>Using branch width: 0.431 (width.scale.factor: 1.5)<br>Outliers: 0<br>Total number of branches: 1 (forks: 0)<br>Backbone fork merge (width: 0.431): 31 -> 31 <br>Ranking all cells...<br>Computing tree layout...output saved in /scratch/irc/personal/robrechtc/tmp//Rtmplk1Rxc/output: <br> output.rds<br></code>
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