Output¶
SourcePredict result file¶
File: *.sourcepredict.csv
This csv
file contains the predicted proportion of each source in each sample.
Like in any classification problem, the predicted source is the greatest proportion.
Example:
+------------------+----------------------+
| | ERR1915662 |
+------------------+----------------------+
| Canis_familiaris | 0.9449678590674971 |
+------------------+----------------------+
| Homo_sapiens | 0.027033026106258438 |
+------------------+----------------------+
| Soil | 0.014110223165444446 |
+------------------+----------------------+
| unknown | 0.013888891660799834 |
+------------------+----------------------+
While in this example it is pretty clear that the ERR1915662
sample is likely a dog, you may face situations where it will be less obvious. Looking at the embedding can therefore be useful to decide from which source(s) the sink sample is made up of.
Embedding csv file¶
This csv
file contains the embedding of training in test samples in lower dimensions by TSNE or UMAP
Example:
+-----------------+------------+-------------+--------------+-----------------+
| | PC1 | PC2 | labels | name |
+-----------------+------------+-------------+--------------+-----------------+
| SRR1175007 | -28.858526 | 0.59231776 | Homo_sapiens | SRR1175007 |
+-----------------+------------+-------------+--------------+-----------------+
| SRR042182 | -22.14415 | -0.47057405 | Homo_sapiens | SRR042182 |
+-----------------+------------+-------------+--------------+-----------------+
| SRR061154 | -30.210106 | -2.0323594 | Homo_sapiens | SRR061154 |
+-----------------+------------+-------------+--------------+-----------------+
| SRR061499 | -25.546652 | 0.27987793 | Homo_sapiens | SRR061499 |
+-----------------+------------+-------------+--------------+-----------------+
| SRR063469 | -22.88011 | 1.1526666 | Homo_sapiens | SRR063469 |
+-----------------+------------+-------------+--------------+-----------------+
| SRR062324 | -25.50832 | -0.25076494 | Homo_sapiens | SRR062324 |
+-----------------+------------+-------------+--------------+-----------------+
| SRR1179037 | -28.779644 | 0.1385772 | Homo_sapiens | SRR1179037 |
+-----------------+------------+-------------+--------------+-----------------+
| SRR061236 | -29.470839 | -0.8973783 | Homo_sapiens | SRR061236 |
+-----------------+------------+-------------+--------------+-----------------+
| SRR061456 | -28.31991 | -0.9834692 | Homo_sapiens | SRR061456 |
+-----------------+------------+-------------+--------------+-----------------+
| SRR1761669 | 4.1411834 | 14.485897 | Homo_sapiens | SRR1761669 |
+-----------------+------------+-------------+--------------+-----------------+
| SRR1761668 | 1.7706155 | 13.6566925 | Homo_sapiens | SRR1761668 |
+-----------------+------------+-------------+--------------+-----------------+
| SRR1761675 | 3.2434833 | 16.020077 | Homo_sapiens | SRR1761675 |
+-----------------+------------+-------------+--------------+-----------------+
| SRR3578625 | 24.127249 | 17.996181 | Soil | SRR3578625 |
+-----------------+------------+-------------+--------------+-----------------+
| ERR1939165 | 28.738718 | 19.882471 | Soil | ERR1939165 |
+-----------------+------------+-------------+--------------+-----------------+
| SRR3578645 | 24.138885 | 17.998867 | Soil | SRR3578645 |
+-----------------+------------+-------------+--------------+-----------------+
| ERR1915662 | -14.770308 | -30.94284 | sink | ERR1915662 |
+-----------------+------------+-------------+--------------+-----------------+
See the example usage of Sourcepredict for a example of how to plot it.