**130**wrote:

In this graph 81 cells have being ordered by pseudo time. For example cell s0.76 has been placed at the start of pseudo time and cell s0.11 placed at the end of pseudo time.

This is the expression profile of this gene on this pseudo time

```
> Data
s0.76 s0.52 s0.72 s0.36 s0.18 s0.60 s0.54 s0.65 s0.56 s0.4 s0.14 s0.67 s0.1 s0.22 s0.28 s0.80 s0.16 s0.32
6354.316 2376.278 8037.063 4879.946 4989.872 5382.370 13239.227 12085.752 5510.481 9311.501 5303.664 13480.634 9085.402 9585.708 12678.642 8595.338 13901.138 9809.339
s0.8 s0.55 s0.71 s0.41 s0.40 s0.48 s0.68 s0.81 s0.29 s0.78 s0.34 s0.42 s0.13 s0.9 s0.7 s0.24 s0.62 s0.35
12554.518 11001.622 6676.949 9266.956 5303.998 13405.392 8327.440 6903.236 9319.111 4427.627 11029.422 5370.687 4854.454 13199.522 5125.644 11687.103 7546.622 8656.206
s0.23 s0.21 s0.37 s0.25 s0.79 s0.64 s0.44 s0.15 s0.43 s0.63 s0.10 s0.6 s0.19 s0.31 s0.38 s0.39 s0.73 s0.59
4578.953 15771.795 3217.201 6362.859 11523.728 5977.613 4805.703 5373.737 2393.996 9104.929 3532.215 7974.742 4949.271 3285.566 10896.503 3746.348 4296.337 6510.001
s0.2 s0.12 s0.61 s0.66 s0.51 s0.58 s0.50 s0.27 s0.77 s0.69 s0.33 s0.17 s0.74 s0.26 s0.57 s0.49 s0.70 s0.53
3728.896 8761.615 3896.014 2618.151 4106.299 11898.634 2978.410 3129.880 5571.995 4314.655 3867.158 2209.066 1723.784 2741.320 4570.466 5506.473 3120.334 7284.682
s0.30 s0.45 s0.5 s0.47 s0.46 s0.75 s0.20 s0.3 s0.11
9454.997 7446.095 4765.971 7861.282 10393.357 4809.735 12421.501 12615.785 22238.399
```

Now, my question is, how I could color the plot by knowing a set of cells are in G2 and another set are in S/M phase of cell cycle like this picture?

These cells are at G2

```
[1] "s0.1" "s0.2" "s0.3" "s0.6" "s0.7" "s0.8" "s0.9" "s0.10" "s0.12" "s0.13" "s0.14" "s0.15" "s0.16" "s0.19" "s0.21" "s0.22" "s0.23" "s0.24" "s0.25" "s0.28" "s0.29" "s0.31"
[23] "s0.32" "s0.34" "s0.35" "s0.37" "s0.38" "s0.39" "s0.42" "s0.43" "s0.44" "s0.48" "s0.50" "s0.51" "s0.54" "s0.55" "s0.56" "s0.59" "s0.60" "s0.61" "s0.62" "s0.63" "s0.64" "s0.65"
[45] "s0.66" "s0.67" "s0.68" "s0.70" "s0.71" "s0.73" "s0.78" "s0.79" "s0.80" "s0.81"
```

these cells are in M/S

```
[1] "s0.4" "s0.5" "s0.11" "s0.17" "s0.18" "s0.20" "s0.26" "s0.27" "s0.30" "s0.33" "s0.36" "s0.40" "s0.41" "s0.45" "s0.46" "s0.47" "s0.49" "s0.52" "s0.53" "s0.57" "s0.58" "s0.69"
[23] "s0.72" "s0.74" "s0.75" "s0.76" "s0.77"
```

I tried to do that by this codes but the order of cells is not based on the pseudo time

```
> head(data)
value cell capture
1 30.59486 s0.76 G2
2 78.12876 s0.52 G2
3 63.36236 s0.72 G2
4 54.48303 s0.36 m/s
5 196.49463 s0.18 m/s
6 59.76789 s0.60 G2
>
```

```
> p=ggplot(data, aes(x=cell, y=value, color=capture))
> p+geom_point(alpha=.3)
```