Analysis Report | scPlus v.2.0
Sample: Arabidopsis thaliana leaves
Genome Alignment and Quality Control
Below are key metrics regarding the sample quality.
Number of Reads |
272,739,738 |
Percentage of Reads with Valid Barcodes |
90.38% |
Reads Mapped to Genome |
87.70% |
Reads Mapped to Genes |
74.10% |
Unique Reads in Cells Mapped to Gene + Introns |
98,610,138 |
Estimated Number of Cells |
5,868 |
Mean UMI per Cell |
3,848 |
Median UMI per Cell |
2,399 |
Mean Genes per Cell |
1,235 |
Median Genes per Cell |
996 |
Total Detected Genes |
18,947 |
Clustering
Summary of the clustering results. The table shows the best clustering according to the modularity value and silhouette score. Both scores are contained between zero and one, and the higher the score, the better the clustering. Note that while the resolution parameter is shown, due to it has major impact on the clustering results, other tested parameters have been omitted for brevity.
| Rank | Resolution | N of clusters | Modularity score | Silhouette score |
|---|---|---|---|---|
1st |
0.2 |
11 |
0.94 |
0.171 |
2nd |
0.3 |
13 |
0.94 |
0.171 |
3rd |
0.4 |
15 |
0.93 |
0.172 |
4th |
0.4 |
14 |
0.92 |
0.174 |
5th |
0.2 |
10 |
0.94 |
0.158 |
For each of the best-ranked clusters, a UMAP plot is shown below. The number of cells per cluster is also shown as well as the three best cell type predictions for each cluster.
Rank 1 - Clusters Summary
| UMAP Plot | Number of cells per cluster | ||||||||||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
|
Cell Type Prediction Summary
Confidence of the cell-type prediction is shown in parenthesis. The higher the value, the more confident the prediction.
| Cluster | Cell Type 1 | Cell Type 2 | Cell Type 3 |
|---|---|---|---|
0 |
Mesophyll (52.2) |
Stem cell niche (44.6) |
Phloem parenchyma (44.03) |
1 |
Leaf pavement cell (87.28) |
Leaf epidermis (60.06) |
Non-hair (59.13) |
2 |
Phloem parenchyma (82.33) |
Xylem pole pericycle (78.6) |
Phloem (76.38) |
3 |
Phloem parenchyma (61.46) |
Xylem (56.36) |
Mesophyll (54.76) |
4 |
Phloem parenchyma (89.61) |
Xylem (89.24) |
Protoxylem (83.05) |
5 |
Leaf guard cell (88.14) |
Lateral root cap (45.23) |
Root cap (43.45) |
6 |
Leaf pavement cell (59.38) |
Leaf epidermis (58.78) |
Lateral root cap (45.16) |
7 |
Phloem parenchyma (84.91) |
Phloem (69.75) |
Xylem (69.18) |
8 |
Mesophyll (73.75) |
Palisade mesophyll (64.44) |
S phase (55.8) |
9 |
Companion cell (91.76) |
Phloem (90.89) |
Vascular tissue (53.41) |
10 |
Lateral root cap (46.72) |
Leaf guard cell (45.05) |
Xylem (43.47) |
Rank 2 - Clusters Summary
| UMAP Plot | Number of cells per cluster | ||||||||||||||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
|
Cell Type Prediction Summary
Confidence of the cell-type prediction is shown in parenthesis. The higher the value, the more confident the prediction.
| Cluster | Cell Type 1 | Cell Type 2 | Cell Type 3 |
|---|---|---|---|
0 |
Mesophyll (52.2) |
Stem cell niche (44.6) |
Phloem parenchyma (44.03) |
1 |
Leaf pavement cell (87.28) |
Leaf epidermis (60.06) |
Non-hair (59.13) |
2 |
Phloem parenchyma (81.42) |
Xylem pole pericycle (78.82) |
Phloem (76.61) |
3 |
Phloem parenchyma (62.52) |
Xylem (57.41) |
Mesophyll (54.76) |
4 |
Leaf guard cell (88.14) |
Lateral root cap (45.23) |
Root cap (43.45) |
5 |
Xylem (69.02) |
Phloem parenchyma (65) |
Phloem pole pericycle (59.29) |
6 |
Leaf pavement cell (60.42) |
Leaf epidermis (58.78) |
Lateral root cap (43.11) |
7 |
Phloem parenchyma (84.91) |
Phloem (69.75) |
Xylem (68.15) |
8 |
Mesophyll (74.42) |
Palisade mesophyll (64.5) |
Hydathodes (55.99) |
9 |
Xylem (86.33) |
Phloem parenchyma (76.81) |
Protoxylem (70.2) |
10 |
Phloem (86.84) |
Companion cell (81.86) |
Xylem pole pericycle (53.68) |
11 |
Companion cell (95.66) |
Phloem (82) |
Vascular tissue (72.55) |
12 |
Leaf guard cell (47.6) |
Lateral root cap (45.16) |
Xylem (43.93) |
Rank 3 - Clusters Summary
| UMAP Plot | Number of cells per cluster | ||||||||||||||||||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
|
Cell Type Prediction Summary
Confidence of the cell-type prediction is shown in parenthesis. The higher the value, the more confident the prediction.
| Cluster | Cell Type 1 | Cell Type 2 | Cell Type 3 |
|---|---|---|---|
0 |
Mesophyll (52.2) |
Stem cell niche (44.6) |
Phloem parenchyma (44.03) |
1 |
Leaf pavement cell (79.91) |
Leaf epidermis (65.78) |
Lateral root cap (65.43) |
2 |
Phloem (84.46) |
Phloem parenchyma (82.97) |
Xylem pole pericycle (81.53) |
3 |
Phloem parenchyma (62.52) |
Xylem (57.41) |
Mesophyll (54.76) |
4 |
Leaf guard cell (88.14) |
Lateral root cap (45.23) |
Root cap (43.45) |
5 |
Xylem (66.02) |
Phloem parenchyma (63.98) |
Mesophyll (59.15) |
6 |
Leaf pavement cell (60.42) |
Leaf epidermis (58.78) |
Lateral root cap (43.11) |
7 |
Phloem parenchyma (84.91) |
Phloem (68.71) |
Xylem (68.15) |
8 |
Mesophyll (74.2) |
Palisade mesophyll (64.06) |
S phase (55.6) |
9 |
Xylem (87.3) |
Phloem parenchyma (75.83) |
Protoxylem (70.2) |
10 |
Leaf pavement cell (91.8) |
Leaf epidermis (52.42) |
Leaf guard cell (49.64) |
11 |
Mesophyll (63.81) |
Root cortex (62.11) |
Leaf guard cell (61.2) |
12 |
Phloem (86.84) |
Companion cell (81.86) |
Xylem pole pericycle (53.68) |
13 |
Companion cell (95.66) |
Phloem (82) |
Vascular tissue (72.55) |
14 |
Leaf guard cell (47.6) |
Lateral root cap (45.16) |
Xylem (43.93) |
Rank 4 - Clusters Summary
| UMAP Plot | Number of cells per cluster | ||||||||||||||||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
|
Cell Type Prediction Summary
Confidence of the cell-type prediction is shown in parenthesis. The higher the value, the more confident the prediction.
| Cluster | Cell Type 1 | Cell Type 2 | Cell Type 3 |
|---|---|---|---|
0 |
Mesophyll (52.2) |
Stem cell niche (44.6) |
Phloem parenchyma (44.03) |
1 |
Phloem (82.7) |
Phloem parenchyma (81.24) |
Xylem pole pericycle (79.83) |
2 |
Leaf pavement cell (79.7) |
Lateral root cap (65.07) |
Non-hair (63.26) |
3 |
Xylem (89.24) |
Phloem parenchyma (88.63) |
Protoxylem (82.06) |
4 |
Leaf guard cell (88.14) |
Lateral root cap (45.23) |
Root cap (43.45) |
5 |
Mesophyll (61.06) |
Xylem (45.88) |
Bundle sheath (40.17) |
6 |
Leaf pavement cell (59.38) |
Leaf epidermis (58.78) |
Lateral root cap (44.14) |
7 |
Phloem parenchyma (84.91) |
Phloem (69.75) |
Xylem (69.18) |
8 |
Mesophyll (74.42) |
Palisade mesophyll (64.5) |
S phase (54.91) |
9 |
Leaf pavement cell (91.8) |
Leaf epidermis (52.42) |
Leaf guard cell (49.64) |
10 |
Mesophyll (63.81) |
Root cortex (63.2) |
Leaf guard cell (60.1) |
11 |
Phloem (86.84) |
Companion cell (81.86) |
Xylem pole pericycle (53.68) |
12 |
Companion cell (94.69) |
Phloem (81.02) |
Vascular tissue (70.53) |
13 |
Leaf guard cell (47.6) |
Lateral root cap (45.16) |
Xylem (43.93) |
Rank 5 - Clusters Summary
| UMAP Plot | Number of cells per cluster | ||||||||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
|
Cell Type Prediction Summary
Confidence of the cell-type prediction is shown in parenthesis. The higher the value, the more confident the prediction.
| Cluster | Cell Type 1 | Cell Type 2 | Cell Type 3 |
|---|---|---|---|
0 |
Xylem (66.56) |
Mesophyll (64.53) |
Phloem parenchyma (64.26) |
1 |
Mesophyll (52.2) |
Stem cell niche (44.6) |
Phloem parenchyma (44.03) |
2 |
Leaf pavement cell (86.22) |
Leaf epidermis (61.13) |
Non-hair (58.08) |
3 |
Phloem parenchyma (88.63) |
Xylem (88.27) |
Protoxylem (81.07) |
4 |
Leaf guard cell (88.14) |
Lateral root cap (45.23) |
Root cap (43.45) |
5 |
Leaf pavement cell (58.75) |
Leaf epidermis (57.12) |
Lateral root cap (43.67) |
6 |
Phloem parenchyma (84.91) |
Phloem (69.75) |
Xylem (68.15) |
7 |
Mesophyll (74.2) |
Palisade mesophyll (64.06) |
S phase (55.6) |
8 |
Companion cell (91.8) |
Phloem (90.96) |
Vascular tissue (54.86) |
9 |
Leaf guard cell (47.6) |
Lateral root cap (45.16) |
Xylem (43.93) |