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Examples to run the R package patternize
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Problem running patternize paper example #2

Open RomiPicci opened 4 months ago

RomiPicci commented 4 months ago

Dear Steven, I´m running the script with the examples of the paper introducing patternize and I found a problem. When I run line 376 in the guppies' example, the following sentence appears:

Error in plotHeat(summedRaster_KWT, IDListWT, plotCartoon = TRUE, refShape = "target", : if cartoonID not in image list, please provide image to refImage argument.

I added the argument cartoonID = "cross20_F1fBC1_wtm_9472"

And then the following appears:

Error in plot.new() : figure margins too large

I tried to fix the crop vector (crop = c(200,2800,300,1800)) with several values but the answer is always the same.

Could you give me any tip to fix the issue?

Thanks in advance, Romina

StevenVB12 commented 4 months ago

Dear Romina,

The figure margins too large may just be because your physical plotting window is too small. You would need to increase the plot window manually in Rstudio.

In any case, since the publication of the examples, we have worked on approaches that might work better for you, especially as an alternative to k-means. I would definitely give this a try instead: https://hiweller.rbind.io/post/recolorize-patternize-workflow/

Best regards,

Steven

Van Belleghem Steven From: RomiPicci @.> Sent: Tuesday, 9 July 2024 00:08 To: StevenVB12/patternize-examples @.> Cc: Subscribed @.***> Subject: [StevenVB12/patternize-examples] Problem running patternize paper example (Issue #2)

Dear Steven, I´m running the script with the examples of the paper introducing patternize and I found a problem. When I run line 376 in the guppies' example, the following sentence appears:

Error in plotHeat(summedRaster_KWT, IDListWT, plotCartoon = TRUE, refShape = "target", : if cartoonID not in image list, please provide image to refImage argument.

I added the argument cartoonID = "cross20_F1fBC1_wtm_9472"

And then the following appears:

Error in plot.new() : figure margins too large

I tried to fix the crop vector (crop = c(200,2800,300,1800)) with several values but the answer is always the same.

Could you give me any tip to fix the issue?

Thanks in advance, Romina

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