hello guys, I got a problem when using ggplot2 to draw a bubble graph. I ran the same R codes on two different days, it came out with two different bubble graph results. here is my R codes:
f<-read.xlsx("C:/Users/Washington Lan/Desktop/4173GIC.xlsx","4173")
and here are the two different graph results:
as you can see, I want the result presented as the right one, not the left one. the bubbles on the left graph are disrupted by many black edges, meanwhile the bubbles on the right graph are much more clear than the left graph. both graphs came out with the same R codes as presented above. and I can't get the same graph as the graph on the right side anymore. why is that? what can I do to get the result as the graph on the right side?
Without more information, my guess is that you re-sized the plot window between renderings, making the window smaller — what happens when you increase the size of the plot window?
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firstly, thank you for your reply! the pic on the upside is what I get today, and the pic on the downside is from days ago. both pics were using the same R codes and exported as PDF files using the same parameters, however, their appearances are so different. the pic on the downside has more clear circles, which I preferred. my issue is that, I can't get the pic just like the downside one anymore.
Thank you for resizing the window, @washingtonwuyi , it makes the differences much clearer.
From the images, it seems that the tables used for the two plots are not the same; that is, they may contain the same data, but row order in one plot seems to be different from the row order in the other plot. This is clear, for example, by looking at the purple point near the top of the bottom plot: In the top plot, the same point is drawn under a red point. In ggplot, points that correspond to earlier rows appear under ones that correspond to later rows.
So, to sort out what you need to do to recover your desired plot, it would help if you could share a table with representative data that we can work with.
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I'm so appreciated for your warm-hearted answer! I definitely want to share my table with the raw data in this issue, for it may help to better solve problems. as a new user to this great community, I just figured out how to upload my data (which I'm so sorry).here is my data that used to make the bubble graphs, but it's just a small part of it, for the message body here is limited to 32000 characters; may I send the whole data to you via another way, like e-mailing?
Data
|gene | Length | GIC score | Log2FoldChange | padj|
thank you again! I reordered the data on my Excel table, then re-ran the codes, and the problem had been solved nicely! now we've got a pretty bubble graph~ this issue has been bothering me for days, and I finally got a perfect solution from this forum. may the force be with you @dromano , and may the force be with this amazing and fabulous community!
Glad to see you figured out how to get the plot you wanted! In general, I would recommend doing all your work in R rather than Excel if possible; that way you can always track down exactly what you did before.
And could I ask you to edit the post where you shared your data? It adds a lot of length to the page, but it's easy to make it optionally visible — just place the following markdown text before and after:
[details="Data"]
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thank you for your advice. all done.
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system
April 13, 2024, 9:02pm
10
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