scTyper Report
Report Summary
______________________________________________________________
Project Name : scTyper
Date : 2020-06-04 18:24:49
User : hikim
Processed excuted pipeline : QC (FALSE), CellRanger (FALSE), Normalization (FALSE), Cell Typing (NTP), inferCNV (TRUE)
Input data type : Seurat object
Runtime : 28.8 mins
_______________________________________________________________
scTyper supports a report summarizing for cell typing pipeline. This report provides information of the parameters used to run, samples statistics and visualize assigned cell types using t-SNE plot and heatmap.
1. Parameters used
Global configuration parameters:
Parameters Values proj.name scTyper wd /data/Rpackage/scTyper output.name /Set.test.public.result/public.NTP.cell.T pheno.fn /data/Rpackage/scTyper/data/pheno_info_public.csv qc FALSE run.cellranger FALSE norm.seurat FALSE cell.typing.method NTP level cell run.inferCNV TRUE mc.cores 10 report.mode TRUE
Cell typing parameters:
Parameters Values marker Puram.2017.HNSCC.TME slot scale.data assay RNA NTP.g.filter.method sd NTP.gene.filter.cutoff 0.3 NTP.distance cosine NTP.norm.method none gene.ref.gtf /data/pubdata/ngs_ref/cellranger/refdata-cellranger-GRCh38-1.2.0/genes/genes.gtf feature.to.test cell.type cells.test_excluded c(“Epithelial_cell”, “Unresolved_cell”) cells.test_reference c(“Fibroblasts”, “T.cells”, “B_Plasma.cells”, “Macrophages”, “Dendritic.cells”, “Endothelial.cells”, “Myocytes”, “Mast”) fc.cutoff 0.05 malignant.cell.type Epithelial_cell cutoff.gene.cluster 0.05
2. Statistic of the input data
- Number of cells: 5902
- Number of samples: 24
- Sample statistics
| sampleID | Number.of.Cells | Average.count.of.nUMIs | Average.number.of.genes |
|---|---|---|---|
| Cancer_P0 | 259 | 7433 | 3245 |
| Cancer_P10 | 89 | 6983 | 3163 |
| Cancer_P12 | 157 | 6809 | 3355 |
| Cancer_P13 | 90 | 9422 | 4060 |
| Cancer_P16 | 596 | 8819 | 3757 |
| Cancer_P17 | 490 | 11705 | 4900 |
| Cancer_P18 | 567 | 8876 | 3719 |
| Cancer_P20 | 345 | 15332 | 6174 |
| Cancer_P22 | 201 | 11070 | 4494 |
| Cancer_P23 | 51 | 6626 | 2352 |
| Cancer_P24 | 130 | 9196 | 3853 |
| Cancer_P25 | 434 | 10084 | 4139 |
| Cancer_P26 | 130 | 9683 | 4008 |
| Cancer_P28 | 370 | 9335 | 3428 |
| Cancer_P5 | 213 | 11520 | 4604 |
| Cancer_P6 | 308 | 12237 | 4924 |
| Cancer_P7 | 7 | 11067 | 5089 |
| Cancer_P8 | 104 | 7648 | 3504 |
| LymphNode_P0 | 23 | 7240 | 2787 |
| LymphNode_P20 | 346 | 13835 | 5503 |
| LymphNode_P25 | 291 | 9168 | 4067 |
| LymphNode_P26 | 298 | 11601 | 5158 |
| LymphNode_P28 | 246 | 10901 | 4449 |
| LymphNode_P5 | 157 | 12026 | 4842 |
3. Result of pre-processing
[1] "FastQC process is skipped"4. Result of cellranger - summary metrics
[1] "CellRanger process is skipped"5. Result of cell typing
scTyper provides three cell typing methods of the nearest template prediction (NTP), enrichment scores(ES) and average values for cell markers. Cell types are assigned according to the marker gene and cell typing method specified by the user as parameters.
5-1. Cell typing methods and cell markers used
- Cell typing method: NTP
- infer-CNV Malignant cell typing: Yes
Cell marker sets: Puram.2017.HNSCC.TME
- T_cell: CD2, CD3D, CD3E and CD3G
- B_Plasma_cell: SLAMF7, CD79A, BLNK and FCRL5
- Dendritic_cell: CD40, CD80, CD83 and CCR7
- Endothelial_cell: PECAM1, VWF and ENG
- Epithelial_cell: KRT14, KRT17, KRT6A, KRT5, KRT19, KRT8, KRT16, KRT18, KRT6B, KRT15, KRT6C, KRTCAP3, EPCAM and SFN
- Mast_cell: CMA1, MS4A2, TPSAB1 and TPSB2
- Macrophage: CD14, CD163, CD68, FCGR2A and CSF1R
- Myocyte: ACTA1, ACTN2, MYL2 and MYH2
- Fibroblast: FAP, PDPN, COL1A2, DCN, COL3A1 and COL6A1
5-2. Cell type statistics
In malignant cell typing, a total 2739 malignant cells were assigned by NTP (n= 2332), or inferCNV (n= 2618)
Cell type statistics across samples
| Total | Cancer_P0 | Cancer_P10 | Cancer_P12 | Cancer_P13 | Cancer_P16 | Cancer_P17 | Cancer_P18 | Cancer_P20 | Cancer_P22 | Cancer_P23 | Cancer_P24 | Cancer_P25 | Cancer_P26 | Cancer_P28 | Cancer_P5 | Cancer_P6 | Cancer_P7 | Cancer_P8 | LymphNode_P0 | LymphNode_P20 | LymphNode_P25 | LymphNode_P26 | LymphNode_P28 | LymphNode_P5 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| B_Plasma_cell | 190 | 5 | 44 | 2 | 10 | 12 | 6 | 18 | 0 | 0 | 0 | 0 | 6 | 0 | 0 | 3 | 4 | 0 | 13 | 12 | 0 | 27 | 3 | 22 | 3 |
| Dendritic_cell | 221 | 17 | 4 | 12 | 35 | 24 | 8 | 30 | 0 | 5 | 0 | 1 | 30 | 2 | 8 | 5 | 1 | 0 | 10 | 1 | 0 | 20 | 4 | 2 | 2 |
| Endothelial_cell | 249 | 2 | 7 | 0 | 2 | 36 | 18 | 18 | 2 | 1 | 0 | 2 | 5 | 3 | 17 | 8 | 42 | 0 | 26 | 1 | 0 | 9 | 10 | 12 | 28 |
| Fibroblast | 638 | 7 | 23 | 0 | 2 | 57 | 38 | 29 | 7 | 27 | 0 | 57 | 47 | 32 | 106 | 15 | 39 | 1 | 19 | 4 | 0 | 30 | 38 | 52 | 8 |
| Macrophage | 125 | 4 | 1 | 1 | 3 | 13 | 2 | 23 | 1 | 0 | 0 | 4 | 5 | 2 | 9 | 41 | 3 | 0 | 3 | 0 | 0 | 4 | 1 | 4 | 1 |
| Malignant_cell | 2739 | 20 | 5 | 12 | 16 | 102 | 357 | 214 | 329 | 123 | 0 | 30 | 191 | 63 | 78 | 108 | 211 | 6 | 12 | 0 | 343 | 91 | 217 | 112 | 99 |
| Mast_cell | 125 | 6 | 1 | 0 | 4 | 25 | 7 | 12 | 0 | 22 | 0 | 20 | 11 | 1 | 0 | 4 | 1 | 0 | 3 | 1 | 0 | 3 | 0 | 2 | 2 |
| Myocyte | 51 | 2 | 0 | 0 | 0 | 4 | 0 | 2 | 0 | 0 | 0 | 0 | 15 | 1 | 16 | 1 | 0 | 0 | 0 | 0 | 0 | 5 | 1 | 4 | 0 |
| T_cell | 1008 | 184 | 0 | 121 | 10 | 269 | 45 | 161 | 0 | 0 | 50 | 0 | 66 | 3 | 0 | 23 | 0 | 0 | 18 | 1 | 0 | 56 | 1 | 0 | 0 |
| Unresolved_cell | 556 | 12 | 4 | 9 | 8 | 54 | 9 | 60 | 6 | 23 | 1 | 16 | 58 | 23 | 136 | 5 | 7 | 0 | 0 | 3 | 3 | 46 | 23 | 36 | 14 |
5-3. Distribution of cell types
Distribution of inferred cell types
Distibution of cell types across samples
t-SNE plots
- Inferred cell types by NTP
- Malignant cells by inferCNV
- CNV score by inferCNV
- Seurat clusters
- Samples
- Cell markers heatmap
A heatmap shows the cell typing result and the gene expression levels of cell marker gene sets from Puram.2017.HNSCC.TME. For each method, the assigned cell types are indicated by color bars.
