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6.2 years ago
Za
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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)
Just a few observations that I wish to share with you:
Your question was extremely specific and generic at the same time. You could have searched Stack Overflow for
color scatter plot by attributeand you'd have gotten the answer with a tiny bit of digging. All of the context you provided in the post is of little value to users here, as the context is singular to your use case. You should work on providing a simple, reproducible example with dummy data, not the details of your actual context.This leads to the second point. When your question and answer are within an hour of each other, you're using us as a shortcut and not really contributing to the knowledge content of the site. And this behavior was also seen in your previous account. I strongly recommend you try harder before you post here, and when you do create a post, have the post be reproducible and valuable as a knowledge item.
Thank you!
You definitely you alright. Honestly, biostars is always my bests way of documentation for solutions for similar questions in future because I would always refer to my posts in near future. But believe me I am posting my question firstly here as I don't have any hope that I would find the solution myself and most of time I have to find the solution in a defined short time frame. So I post my question here and I am going to find the solution myself. In 90% of my posts I can not find the solution myself and here biostars solve the problem. Only one point, I am not mis using this website at all, at least not intentionally.
You are off course welcome to ask your questions here. But as Ram said, this one wasn't too hard and could have been solved easily. It is no use to be stuck on a problem for days, but spending a few hours is not wrong. Quite the contrary: every next question you'll have to solve will be easier because you learned how to figure things out.
Can you edit your question and answer to make them a bit more generic, as Ram suggested? As such more users in the future will be helped by stumbling upon this question in their own journey.