Calculate Average Gene Expression¶
-
calculateMetaTable()
Function to calculate 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
)
Arguments¶
gobject |
giotto object |
expression_values |
expression values to use |
metadata_cols |
annotation columns found in pDataDT(gobject) |
selected_genes |
subset of genes to use |
Value¶
A data.table with average expression values for each gene per (combined) annotation
Examples¶
data(mini_giotto_single_cell)
Show cell metadata
pDataDT(mini_giotto_single_cell)
#> 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