Details
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Type:
Task
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Status: Closed (View Workflow)
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Priority:
Major
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Resolution: Done
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Affects Version/s: None
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Fix Version/s: None
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Labels:None
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Story Points:2
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Epic Link:
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Sprint:Fall 1 - Sep 5, Summer 6 2023 July 24, Summer 7 2023 Aug 7, Summer 8 2023 Aug 21
Description
Dr. Loraine comments:
- Figure out a nicer way to present the result from sanity checking. Currently, the message letting the reader know that the test passed does not fit on the page, making it harder to follow what is going on. See: p. 3, Muday-DESeq-PCA-Plots.pdf
- First two words of the section of text appearing after the plot are confusing. It says: "The following plot.." suggesting the plot will be after this text. But the plot is actually appearing before the text, not after it. However, there is only one plot, so it's obvious what the text is talking about.
- To me, this statement describing part "A" sounds nonsensical: "We also see that over a longer duration of time that there is even more significant variance between the samples." I see filled shapes spread about evenly across the two "slash"-shaped clusters. There is no such trend. Also, I don't think there is something such as "significant variance" in the statistical sense. Maybe you mean to say: "a lot" ?
- Regarding "B": I agree with the statement made about temperature. I recommend wording it a little differently to refer back to the image itself a bit more. How about: "PC1 cleanly separates points into two visually obvious groups, one containing only earlier-stage sample points and the second containing only-later-stage points."
- Regarding "C": I agree, there's no trend here. There are two, maybe three clusters, plus a singleton. Not obvious trends are there with respect to any of the variables examined. The current statement: "C) The OE3 genotype was an analysis of just OE3 samples and had no clear indication of clustering or separation of points except for maybe a little at 75 minutes." is correct. But I think you should change the word "just" to "only," or, better yet, say "This plot and the code used to produce it included OE3 genotype samples only." Also, we can easily check this is true by looking at the included code.
- Regarding "D": There's an obvious visual separation between the treatment (heat stress) samples and the control (no-heat stress sample) in the PC2 dimension. There is also a clear grouping based on early-versus-later sample points in the PC1 dimension. Editorial comment: feel "D" is the most exciting image.
- This statement again needs to be connected to the plot itself: "The ARE genotype has the largest variation out of all PCA plots and was analyzed with just ARE samples." Why do you say this about variance? How can the reader make the same conclusion about variance for themselves. What do they need to look at in the image? Explain this better and talk about what it means in the Discussion. Recall that the true "result" here is your observation about what the plot looks like.
Comments on the Discussion:
- First sentence is just filler. Remove it.
- Second sentence has a lot of filler words. Reword it to remove unnecessary words. Change: "The goal was to answer these questions for the experiment to be successful:" to "Question (or questions) this Markdown aims to answer:"
- There are a lot of things an author can do with a Discussion, but the ultimate goal should be the same in each case: Explain the Results.
- There are a lot of choices about how to organize a Discussion section. Here are some:
- Re-list the questions from the Introduction.
- Edit by including one or two paragraphs following each question stating the answer to the question, and evidence. Interleave answers so that each re-stated question is followed by its answer and evidence for the answer.
- Then list the questions, one-by-one, and say what the answer is, using the Results.
- If the question is: "Was the experiment successful" and you have arrived at an answer to this question, you have to explain it more.
I feel it is too vague, anyway.
Suggestion: Read the comments and then spend an afternoon or a couple of hours to make some improvements. If you like it better, submit a new PR. If you don't, we can close this.
As far as I am concerned, I feel I can look at the plots and come to my own conclusions about them. I don't need a Markdown to explain it to me, because I can read code and understand it, generally. Someone else might not, however. I would recommend investing at least another half-day in making improvements, but not much more, unless Molly Davis thinks more or less is needed.
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| Field | Original Value | New Value |
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| Description |
*Dr. Loraine comments*:
Figure out a nicer way to present the result from sanity checking. Currently, the message letting the reader know that the test passed does not fit on the page, making it harder to follow what is going on. See: p. 3, Muday-DESeq-PCA-Plots.pdf First two words of the section of text appearing after the plot are confusing. It says: "The following plot.." suggesting the plot will be after this text. But the plot is actually appearing before the text, not after it. However, there is only one plot, so it's obvious what the text is talking about. To me, this statement describing part "A" sounds nonsensical: "We also see that over a longer duration of time that there is even more significant variance between the samples." I see filled shapes spread about evenly across the two "slash"-shaped clusters. There is no such trend. Also, I don't think there is something such as "significant variance" in the statistical sense. Maybe you mean to say: "a lot" ? Regarding "B": I agree with the statement made about temperature. I recommend wording it a little differently to refer back to the image itself a bit more. How about: "PC1 cleanly separates points into two visually obvious groups, one containing only earlier-stage sample points and the second containing only-later-stage points." Regarding "C": I agree, there's no trend here. There are two, maybe three clusters, plus a singleton. Not obvious trends are there with respect to any of the variables examined. The current statement: "C) The OE3 genotype was an analysis of just OE3 samples and had no clear indication of clustering or separation of points except for maybe a little at 75 minutes." is correct. But I think you should change the word "just" to "only," or, better yet, say "This plot and the code used to produce it included OE3 genotype samples only." Also, we can easily check this is true by looking at the included code. Regarding "D": There's an obvious visual separation between the treatment (heat stress) samples and the control (no-heat stress sample) in the PC2 dimension. There is also a clear grouping based on early-versus-later sample points in the PC1 dimension. Editorial comment: feel "D" is the most exciting image. This statement again needs to be connected to the plot itself: "The ARE genotype has the largest variation out of all PCA plots and was analyzed with just ARE samples." Why do you say this about variance? How can the reader make the same conclusion about variance for themselves. What do they need to look at in the image? Explain this better and talk about what it means in the Discussion. Recall that the true "result" here is your observation about what the plot looks like. Comments on the Discussion: First sentence is just filler. Remove it. Second sentence has a lot of filler words. Reword it to remove unnecessary words. Change: "The goal was to answer these questions for the experiment to be successful:" to "Question (or questions) this Markdown aims to answer:" More thoughts: There are a lot of things an author can do with a Discussion, but the ultimate goal should be the same in each case: Explain the Results. There are a lot of choices about how to organize a Discussion section. Here are some: Listify: Re-list the questions from the Introduction. Edit by including one or two paragraphs following each question stating the answer to the question, and evidence. Interleave answers so that each re-stated question is followed by its answer and evidence for the answer. Then list the questions, one-by-one, and say what the answer is, using the Results. If the question is: "Was the experiment successful" and you have arrived at an answer to this question, you have to explain it more. I feel it is too vague, anyway. Suggestion: Read the comments and then spend an afternoon or a couple of hours to make some improvements. If you like it better, submit a new PR. If you don't, we can close this. As far as I am concerned, I feel I can look at the plots and come to my own conclusions about them. I don't need a Markdown to explain it to me, because I can read code and understand it, generally. Someone else might not, however. I would recommend investing at least another half-day in making improvements, but not much more, unless Molly Davis thinks more or less is needed. |
*Dr. Loraine comments*:
* Figure out a nicer way to present the result from sanity checking. Currently, the message letting the reader know that the test passed does not fit on the page, making it harder to follow what is going on. See: p. 3, Muday-DESeq-PCA-Plots.pdf * First two words of the section of text appearing after the plot are confusing. It says: "The following plot.." suggesting the plot will be after this text. But the plot is actually appearing before the text, not after it. However, there is only one plot, so it's obvious what the text is talking about. * To me, this statement describing part "A" sounds nonsensical: "We also see that over a longer duration of time that there is even more significant variance between the samples." I see filled shapes spread about evenly across the two "slash"-shaped clusters. There is no such trend. Also, I don't think there is something such as "significant variance" in the statistical sense. Maybe you mean to say: "a lot" ? * Regarding "B": I agree with the statement made about temperature. I recommend wording it a little differently to refer back to the image itself a bit more. How about: "PC1 cleanly separates points into two visually obvious groups, one containing only earlier-stage sample points and the second containing only-later-stage points." * Regarding "C": I agree, there's no trend here. There are two, maybe three clusters, plus a singleton. Not obvious trends are there with respect to any of the variables examined. The current statement: "C) The OE3 genotype was an analysis of just OE3 samples and had no clear indication of clustering or separation of points except for maybe a little at 75 minutes." is correct. But I think you should change the word "just" to "only," or, better yet, say "This plot and the code used to produce it included OE3 genotype samples only." Also, we can easily check this is true by looking at the included code. * Regarding "D": There's an obvious visual separation between the treatment (heat stress) samples and the control (no-heat stress sample) in the PC2 dimension. There is also a clear grouping based on early-versus-later sample points in the PC1 dimension. Editorial comment: feel "D" is the most exciting image. * This statement again needs to be connected to the plot itself: "The ARE genotype has the largest variation out of all PCA plots and was analyzed with just ARE samples." Why do you say this about variance? How can the reader make the same conclusion about variance for themselves. What do they need to look at in the image? Explain this better and talk about what it means in the Discussion. Recall that the true "result" here is your observation about what the plot looks like. Comments on the Discussion: First sentence is just filler. Remove it. Second sentence has a lot of filler words. Reword it to remove unnecessary words. Change: "The goal was to answer these questions for the experiment to be successful:" to "Question (or questions) this Markdown aims to answer:" More thoughts: There are a lot of things an author can do with a Discussion, but the ultimate goal should be the same in each case: Explain the Results. There are a lot of choices about how to organize a Discussion section. Here are some: Listify: Re-list the questions from the Introduction. Edit by including one or two paragraphs following each question stating the answer to the question, and evidence. Interleave answers so that each re-stated question is followed by its answer and evidence for the answer. Then list the questions, one-by-one, and say what the answer is, using the Results. If the question is: "Was the experiment successful" and you have arrived at an answer to this question, you have to explain it more. I feel it is too vague, anyway. Suggestion: Read the comments and then spend an afternoon or a couple of hours to make some improvements. If you like it better, submit a new PR. If you don't, we can close this. As far as I am concerned, I feel I can look at the plots and come to my own conclusions about them. I don't need a Markdown to explain it to me, because I can read code and understand it, generally. Someone else might not, however. I would recommend investing at least another half-day in making improvements, but not much more, unless Molly Davis thinks more or less is needed. |
| Description |
*Dr. Loraine comments*:
* Figure out a nicer way to present the result from sanity checking. Currently, the message letting the reader know that the test passed does not fit on the page, making it harder to follow what is going on. See: p. 3, Muday-DESeq-PCA-Plots.pdf * First two words of the section of text appearing after the plot are confusing. It says: "The following plot.." suggesting the plot will be after this text. But the plot is actually appearing before the text, not after it. However, there is only one plot, so it's obvious what the text is talking about. * To me, this statement describing part "A" sounds nonsensical: "We also see that over a longer duration of time that there is even more significant variance between the samples." I see filled shapes spread about evenly across the two "slash"-shaped clusters. There is no such trend. Also, I don't think there is something such as "significant variance" in the statistical sense. Maybe you mean to say: "a lot" ? * Regarding "B": I agree with the statement made about temperature. I recommend wording it a little differently to refer back to the image itself a bit more. How about: "PC1 cleanly separates points into two visually obvious groups, one containing only earlier-stage sample points and the second containing only-later-stage points." * Regarding "C": I agree, there's no trend here. There are two, maybe three clusters, plus a singleton. Not obvious trends are there with respect to any of the variables examined. The current statement: "C) The OE3 genotype was an analysis of just OE3 samples and had no clear indication of clustering or separation of points except for maybe a little at 75 minutes." is correct. But I think you should change the word "just" to "only," or, better yet, say "This plot and the code used to produce it included OE3 genotype samples only." Also, we can easily check this is true by looking at the included code. * Regarding "D": There's an obvious visual separation between the treatment (heat stress) samples and the control (no-heat stress sample) in the PC2 dimension. There is also a clear grouping based on early-versus-later sample points in the PC1 dimension. Editorial comment: feel "D" is the most exciting image. * This statement again needs to be connected to the plot itself: "The ARE genotype has the largest variation out of all PCA plots and was analyzed with just ARE samples." Why do you say this about variance? How can the reader make the same conclusion about variance for themselves. What do they need to look at in the image? Explain this better and talk about what it means in the Discussion. Recall that the true "result" here is your observation about what the plot looks like. Comments on the Discussion: First sentence is just filler. Remove it. Second sentence has a lot of filler words. Reword it to remove unnecessary words. Change: "The goal was to answer these questions for the experiment to be successful:" to "Question (or questions) this Markdown aims to answer:" More thoughts: There are a lot of things an author can do with a Discussion, but the ultimate goal should be the same in each case: Explain the Results. There are a lot of choices about how to organize a Discussion section. Here are some: Listify: Re-list the questions from the Introduction. Edit by including one or two paragraphs following each question stating the answer to the question, and evidence. Interleave answers so that each re-stated question is followed by its answer and evidence for the answer. Then list the questions, one-by-one, and say what the answer is, using the Results. If the question is: "Was the experiment successful" and you have arrived at an answer to this question, you have to explain it more. I feel it is too vague, anyway. Suggestion: Read the comments and then spend an afternoon or a couple of hours to make some improvements. If you like it better, submit a new PR. If you don't, we can close this. As far as I am concerned, I feel I can look at the plots and come to my own conclusions about them. I don't need a Markdown to explain it to me, because I can read code and understand it, generally. Someone else might not, however. I would recommend investing at least another half-day in making improvements, but not much more, unless Molly Davis thinks more or less is needed. |
*Dr. Loraine comments*:
* Figure out a nicer way to present the result from sanity checking. Currently, the message letting the reader know that the test passed does not fit on the page, making it harder to follow what is going on. See: p. 3, Muday-DESeq-PCA-Plots.pdf * First two words of the section of text appearing after the plot are confusing. It says: "The following plot.." suggesting the plot will be after this text. But the plot is actually appearing before the text, not after it. However, there is only one plot, so it's obvious what the text is talking about. * To me, this statement describing part "A" sounds nonsensical: "We also see that over a longer duration of time that there is even more significant variance between the samples." I see filled shapes spread about evenly across the two "slash"-shaped clusters. There is no such trend. Also, I don't think there is something such as "significant variance" in the statistical sense. Maybe you mean to say: "a lot" ? * Regarding "B": I agree with the statement made about temperature. I recommend wording it a little differently to refer back to the image itself a bit more. How about: "PC1 cleanly separates points into two visually obvious groups, one containing only earlier-stage sample points and the second containing only-later-stage points." * Regarding "C": I agree, there's no trend here. There are two, maybe three clusters, plus a singleton. Not obvious trends are there with respect to any of the variables examined. The current statement: "C) The OE3 genotype was an analysis of just OE3 samples and had no clear indication of clustering or separation of points except for maybe a little at 75 minutes." is correct. But I think you should change the word "just" to "only," or, better yet, say "This plot and the code used to produce it included OE3 genotype samples only." Also, we can easily check this is true by looking at the included code. * Regarding "D": There's an obvious visual separation between the treatment (heat stress) samples and the control (no-heat stress sample) in the PC2 dimension. There is also a clear grouping based on early-versus-later sample points in the PC1 dimension. Editorial comment: feel "D" is the most exciting image. * This statement again needs to be connected to the plot itself: "The ARE genotype has the largest variation out of all PCA plots and was analyzed with just ARE samples." Why do you say this about variance? How can the reader make the same conclusion about variance for themselves. What do they need to look at in the image? Explain this better and talk about what it means in the Discussion. Recall that the true "result" here is your observation about what the plot looks like. *Comments on the Discussion*: * First sentence is just filler. Remove it. * Second sentence has a lot of filler words. Reword it to remove unnecessary words. Change: "The goal was to answer these questions for the experiment to be successful:" to "Question (or questions) this Markdown aims to answer:" * There are a lot of things an author can do with a Discussion, but the ultimate goal should be the same in each case: Explain the Results. * There are a lot of choices about how to organize a Discussion section. Here are some: * Re-list the questions from the Introduction. * Edit by including one or two paragraphs following each question stating the answer to the question, and evidence. Interleave answers so that each re-stated question is followed by its answer and evidence for the answer. * Then list the questions, one-by-one, and say what the answer is, using the Results. * If the question is: "Was the experiment successful" and you have arrived at an answer to this question, you have to explain it more. I feel it is too vague, anyway. *Suggestion*: Read the comments and then spend an afternoon or a couple of hours to make some improvements. If you like it better, submit a new PR. If you don't, we can close this. As far as I am concerned, I feel I can look at the plots and come to my own conclusions about them. I don't need a Markdown to explain it to me, because I can read code and understand it, generally. Someone else might not, however. I would recommend investing at least another half-day in making improvements, but not much more, unless Molly Davis thinks more or less is needed. |
| Summary | Edit PCA plot markdown and create knitted file | Edit PCA plot markdown and commit knitted file |
| Status | To-Do [ 10305 ] | In Progress [ 3 ] |
| Status | In Progress [ 3 ] | To-Do [ 10305 ] |
| Sprint | Summer 5 2023 July 10 [ 174 ] | Summer 6 2023 July 24 [ 175 ] |
| Status | To-Do [ 10305 ] | In Progress [ 3 ] |
| Story Points | 1 | 2 |
| Status | In Progress [ 3 ] | To-Do [ 10305 ] |
| Status | To-Do [ 10305 ] | In Progress [ 3 ] |
| Sprint | Summer 6 2023 July 24 [ 175 ] | Summer 6 2023 July 24, Summer 7 2023 Aug 7 [ 175, 176 ] |
| Rank | Ranked higher |
| Assignee | Molly Davis [ molly ] |
| Status | In Progress [ 3 ] | Needs 1st Level Review [ 10005 ] |
| Assignee | Robert Reid [ robertreid ] |
-We could add a desc for PCA:
"PCA is an unsupervised learning method and is similar to clustering1—it finds patterns without reference to prior knowledge about whether the samples come from different treatment groups or have phenotypic differences."
(ref = https://www.nature.com/articles/nmeth.4346)
Lines 27-29 (these are the lines when I open it in R, the lines might be different in your env)
This Markdown analyzes RNA-Seq gene expression data from data file
``r counts_fname`` documented in ``r sample_sheet_fname`` using functions from
the DESeq library.
It has weird spacing and extra lines.
This section:
```
The data set analyzed here comes from heat-treated and control samples collected at 15, 30, 45, and 75 minutes of heat treatment. The analysis shown here will investigate if the ARE genotype shows greater variance compared to other genotypes VF36 and OE3.
```
- Libraries
- * *
- Results
Load required library from the Bioconductor project:
``` {r, include=FALSE}
It is casting an error. The problem might be on my end. Could you take a peak in your environment and make sure it is as it should be?
LINES 73,74
Define a function that builds a Experiment Meta data frame
Define a function that builds a Experiment Meta data frame:
Seems redundant.
Lines 95,96
Define a function that tests treatment versus control in samples that have the same variety and treatment duration as well as time duration.
Define a function that tests treatment versus control in samples that have the same variety and treatment duration as well as time duration:
Seems redundant.
Lines 123,124
Define a Function that create PCA plots that show control and treatment groups clusters over the time durations.
Define a Function that create PCA plots that show control and treatment groups clusters over the time durations:
I changed this paragraph here to add brevity. Feel free to use you wish!
_The following PCA plot combines all plots for easier visualization using colors that are colorblind safe.
A) All of the genotypes are plotted on the first figure and were analyzed together. There is an obvious separation between ARE and the other two genotypes OE3 and VF36. We also see that over a longer duration of time we spread in the variance between the samples (points are separating from one another). The temperature effect shows that the filled datapoints cluster together by temperature. Heat stress samples (34C) differ in gene expression when compared to the control (28C).
B) The VF36 genotype in figure B shows only VF36 genotype samples. We see that time impacts the variation but temperature is not as well separated until reaching the final time points.
C) The OE3 genotype shows no clear indication of clustering or separation of points except possibly at 75 minutes.
D) The ARE genotype has the largest variation out of all PCA plots. The clustering separates by both time and temperature. It is clear that the ARE genotype shows a greater change in gene expression compared to the other two genotypes when under heat stress conditions over time. _
Save Results and Export as PDF
-
I still need to tackle discussion paragraph, so ball is still in my court.
I reworked the discussion paragraph a bit:
- Discussion
PCA Plots are useful for evaluating clustering in gene expression patterns. In this experiment, the plots do not show complete separation between groups. We set out to answer these questions:
- Are the samples from the same condition grouped together?
- What percentage of the total variation is explained in first two principal components (PC1, PC2)?
The samples used in this analysis have significant results regarding separation by PC1 and PC2. The ARE genotype contains the most significant samples due to having the highest variance in PC1. ARE samples at 34 degrees Celsius around 45 to 75 minutes had the largest variance of all other samples. This makes the samples the most significant in the dataset.
I would remove these lines:
- Do the samples from the different experimental conditions separate by PC1 and PC2?
If “yes” is the answer to these questions, then the experiment can be considered a success.
If "no" is the answer to these questions, then the experiments can be considered unsuccessful and may require more extreme conditions or different features.
"The results were very informative on how we should move forward with the rnaseq data or how to perform the experiment/study for next time. "
No need for the word "very". It is very superfluous!
"The ARE genotype reacted genomically different compared to the other two genotypes when under heat stress conditions over specific time durations."
Change this to:
The ARE genotype shows a different gene expression pattern compared to the other two genotypes when under heat stress over a time course of 75 minutes.
[~RobertReid] I am unsure if you are looking at my new edits to the markdown. I have previously fixed things you are commenting on so just want to make sure you are looking at the branch link in this ticket. https://bitbucket.org/mdavis4290/molly3-flavonoid-rnaseq/branch/IGBF-3383
| Assignee | Robert Reid [ robertreid ] | Molly Davis [ molly ] |
Notes from scrum: [~molly] needs to provide explicit step-by-step instructions on how to find the document needed to review.
This link goes directly to the new updated markdown: https://bitbucket.org/mdavis4290/molly3-flavonoid-rnaseq/src/3ca9db2487aee7e53fa0c8b04e006f80780d5673/72_F3H_PollenTube/Muday-DESeq-PCA-Plots.Rmd
Make sure to go to the three dots next to edit and click 'open raw' to download the file. I am sorry for any confusion. Thank you for your help!
| Assignee | Molly Davis [ molly ] | Robert Reid [ robertreid ] |
For PCA plots section, separate the A) B) etc to a new line each time.
A).......
B)......
C)
D)
Makes it more readable!
Otherwise, this looks great!
| Status | Needs 1st Level Review [ 10005 ] | First Level Review in Progress [ 10301 ] |
| Assignee | Robert Reid [ robertreid ] | Molly Davis [ molly ] |
| Status | First Level Review in Progress [ 10301 ] | To-Do [ 10305 ] |
| Status | To-Do [ 10305 ] | In Progress [ 3 ] |
| Assignee | Molly Davis [ molly ] |
| Status | In Progress [ 3 ] | Needs 1st Level Review [ 10005 ] |
| Status | Needs 1st Level Review [ 10005 ] | First Level Review in Progress [ 10301 ] |
| Status | First Level Review in Progress [ 10301 ] | Ready for Pull Request [ 10304 ] |
| Status | Ready for Pull Request [ 10304 ] | Pull Request Submitted [ 10101 ] |
| Assignee | Ann Loraine [ aloraine ] |
| Status | Pull Request Submitted [ 10101 ] | Reviewing Pull Request [ 10303 ] |
| Status | Reviewing Pull Request [ 10303 ] | Merged Needs Testing [ 10002 ] |
| Assignee | Ann Loraine [ aloraine ] |
Changes are merged.
Suggestions on how to test:
- Using your own system, build Muday-DESeq-PCA.Rmd to create a new file Muday-DESeq-PCA.pdf. Install dependencies as needed. Likely the most obnoxious one will be the PDF generator. Ask MD for help if required.
- Compare content in your newly built Muday-DESeq-PCA.pdf to content of Muday-DESeq-PCA.pdf from commit f49ae22. They should be close.
attn: [~molly] Please add additional testing notes as you see fit.
| Sprint | Summer 6 2023 July 24, Summer 7 2023 Aug 7 [ 175, 176 ] | Summer 6 2023 July 24, Summer 7 2023 Aug 7, Summer 8 2023 Aug 21 [ 175, 176, 177 ] |
| Rank | Ranked higher |
| Comment |
[ I am trying the approach shown in Section 3.3 of [edgeRUsersGuide.pdf|https://bioconductor.org/packages/release/bioc/vignettes/edgeR/inst/doc/edgeRUsersGuide.pdf]
I am going to work on it for a few more hours and then call it quits for the day. (¡Mi clase de español empieza a las siete!) I think we ought to try this same linear modeling approach using the two libraries, using code that produces equivalent outputs, and then compare results. Others would probably want to read about it. ] |
change requests:
- Please delete this sentence: "The following PCA plots are combined onto one figure for easier visualization and contain colors that are colorblind safe."
- Please investigate: What code is making "Muday-144-Combined-PCA-Plots.pdf" ? Was this from an earlier version of this script, a version that is no longer current? Is it no longer necessary? If yes, just go ahead and remove it. If we do need to keep it around, let's make a new ticket to track the additional work required to investigate further
- The title shown in the Markdown is not very user-friendly because it uses our internal jargon "PCA Plot Muday lab 72_F3H_PollenTube Data" I recommend a title that summarize the major finding of the report. For example, maybe this?
"Principal components analysis separates RNA-Seq samples by experimental variables" - Knit the Markdown and add the PDF to the repository in the next iteration please. I think it is ready now
| Status | Merged Needs Testing [ 10002 ] | Post-merge Testing In Progress [ 10003 ] |
| Status | Post-merge Testing In Progress [ 10003 ] | To-Do [ 10305 ] |
| Assignee | Molly Davis [ molly ] |
| Sprint | Summer 6 2023 July 24, Summer 7 2023 Aug 7, Summer 8 2023 Aug 21 [ 175, 176, 177 ] | Testing 2 : 4 Nov - 15 Nov, Summer 6 2023 July 24, Summer 7 2023 Aug 7, Summer 8 2023 Aug 21 [ 82, 175, 176, 177 ] |
| Rank | Ranked higher |
| Status | To-Do [ 10305 ] | In Progress [ 3 ] |
Branch: https://bitbucket.org/mdavis4290/molly3-flavonoid-rnaseq/branch/IGBF-3383d
Note: The code is now showing in the markdown of how "Muday-144-Combined-PCA-Plots.pdf" is made. The pdf file contains just the plots so the collaborators have a clear image of the pca plots that can be used in papers.
| Assignee | Molly Davis [ molly ] |
| Status | In Progress [ 3 ] | Needs 1st Level Review [ 10005 ] |
| Assignee | Ann Loraine [ aloraine ] |
| Status | Needs 1st Level Review [ 10005 ] | First Level Review in Progress [ 10301 ] |
| Status | First Level Review in Progress [ 10301 ] | Ready for Pull Request [ 10304 ] |
| Assignee | Ann Loraine [ aloraine ] | Molly Davis [ molly ] |
| Status | Ready for Pull Request [ 10304 ] | Pull Request Submitted [ 10101 ] |
| Assignee | Molly Davis [ molly ] | Ann Loraine [ aloraine ] |
| Status | Pull Request Submitted [ 10101 ] | Reviewing Pull Request [ 10303 ] |
| Status | Reviewing Pull Request [ 10303 ] | Merged Needs Testing [ 10002 ] |
| Status | Merged Needs Testing [ 10002 ] | Post-merge Testing In Progress [ 10003 ] |
| Resolution | Done [ 10000 ] | |
| Status | Post-merge Testing In Progress [ 10003 ] | Closed [ 6 ] |
| Assignee | Ann Loraine [ aloraine ] | Molly Davis [ molly ] |
Branch: https://bitbucket.org/mdavis4290/molly3-flavonoid-rnaseq/branch/IGBF-3383
Reviewer: