calculates the average gene expression for one or more (combined) annotation columns.
calculateMetaTable( gobject, expression_values = c("normalized", "scaled", "custom"), metadata_cols = NULL, selected_genes = NULL )
| gobject | giotto object |
|---|---|
| expression_values | expression values to use |
| metadata_cols | annotation columns found in pDataDT(gobject) |
| selected_genes | subset of genes to use |
data.table with average expression values for each gene per (combined) annotation
#> cell_ID nr_genes perc_genes total_expr leiden_clus cell_types #> 1: cell_2 13 65 111.98320 3 cell C #> 2: cell_7 15 75 115.73030 3 cell C #> 3: cell_12 11 55 95.49802 1 cell A #> 4: cell_15 12 60 99.94782 3 cell C #> 5: cell_17 13 65 111.32963 2 cell B #> 6: cell_30 11 55 96.64302 3 cell C #> 7: cell_37 6 30 57.77777 2 cell B #> 8: cell_40 9 45 82.84693 2 cell B #> 9: cell_44 9 45 79.93838 2 cell B #> 10: cell_53 9 45 82.40747 1 cell A #> 11: cell_64 8 40 73.06345 1 cell A #> 12: cell_74 11 55 93.04295 3 cell C #> 13: cell_85 8 40 73.72574 1 cell A #> 14: cell_86 14 70 115.75186 1 cell A #> 15: cell_90 11 55 93.02181 1 cell A #> 16: cell_95 6 30 59.55714 1 cell A #> 17: cell_96 10 50 88.31757 1 cell A #> 18: cell_107 16 80 130.62640 1 cell A #> 19: cell_113 12 60 99.83100 2 cell B #> 20: cell_118 14 70 117.63523 2 cell B# show average gene expression per annotated cell type calculateMetaTable(mini_giotto_single_cell, metadata_cols = 'cell_types')#> cell_types uniq_ID variable value #> 1: cell C cell C Cldn5 4.262769 #> 2: cell A cell A Cldn5 0.000000 #> 3: cell B cell B Cldn5 4.601433 #> 4: cell C cell C Rtn4r 8.651224 #> 5: cell A cell A Rtn4r 5.670079 #> 6: cell B cell B Rtn4r 2.742910 #> 7: cell C cell C Vgf 8.625694 #> 8: cell A cell A Vgf 9.097362 #> 9: cell B cell B Vgf 1.291685 #> 10: cell C cell C Lingo1 10.013670 #> 11: cell A cell A Lingo1 8.728317 #> 12: cell B cell B Lingo1 3.098198 #> 13: cell C cell C Slc17a7 10.102439 #> 14: cell A cell A Slc17a7 9.879413 #> 15: cell B cell B Slc17a7 5.131600 #> 16: cell C cell C Lynx1 4.814888 #> 17: cell A cell A Lynx1 4.281796 #> 18: cell B cell B Lynx1 2.661027 #> 19: cell C cell C Atp1a1 9.852690 #> 20: cell A cell A Atp1a1 9.800178 #> 21: cell B cell B Atp1a1 4.671602 #> 22: cell C cell C Scg3 0.000000 #> 23: cell A cell A Scg3 3.376464 #> 24: cell B cell B Scg3 8.806105 #> 25: cell C cell C Myh9 3.039197 #> 26: cell A cell A Myh9 2.769607 #> 27: cell B cell B Myh9 5.697493 #> 28: cell C cell C Pcp4l1 5.888908 #> 29: cell A cell A Pcp4l1 4.801477 #> 30: cell B cell B Pcp4l1 2.795894 #> 31: cell C cell C Pygb 1.426957 #> 32: cell A cell A Pygb 3.735340 #> 33: cell B cell B Pygb 8.794492 #> 34: cell C cell C Col4a2 1.229003 #> 35: cell A cell A Col4a2 3.545717 #> 36: cell B cell B Col4a2 7.331353 #> 37: cell C cell C Sdc4 3.271337 #> 38: cell A cell A Sdc4 2.541195 #> 39: cell B cell B Sdc4 7.439861 #> 40: cell C cell C Csf1r 3.089642 #> 41: cell A cell A Csf1r 3.295176 #> 42: cell B cell B Csf1r 3.845324 #> 43: cell C cell C Mtss1l 6.170010 #> 44: cell A cell A Mtss1l 2.532647 #> 45: cell B cell B Mtss1l 7.361713 #> 46: cell C cell C Slc32a1 1.793733 #> 47: cell A cell A Slc32a1 4.012130 #> 48: cell B cell B Slc32a1 0.000000 #> 49: cell C cell C Adarb2 4.278583 #> 50: cell A cell A Adarb2 1.731363 #> 51: cell B cell B Adarb2 1.263504 #> 52: cell C cell C Abtb2 4.278583 #> 53: cell A cell A Abtb2 1.682614 #> 54: cell B cell B Abtb2 2.447522 #> 55: cell C cell C Htra1 6.193813 #> 56: cell A cell A Htra1 1.533463 #> 57: cell B cell B Htra1 6.424891 #> 58: cell C cell C Cplx1 6.486320 #> 59: cell A cell A Cplx1 7.204490 #> 60: cell B cell B Cplx1 5.153216 #> cell_types uniq_ID variable value