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veeninglab / BactMAP

gateway for segmentation data to Rstats & visualization with ggplot2 - in development
http://veeninglab.com/bactmap
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extr_MicrobeJ not working when combining spots & contour CSVs #9

Open vrrenske opened 4 years ago

vrrenske commented 4 years ago

When extracting a CSV containing cell contours and a CSV containing x/y coordinates of Maxima from MicrobeJ, you get an error.

This error is probably resolved in the development version of BactMAP (https://github.com/vrrenske/bactmap). I'll test it for the coming week before putting it in the official version.

Bwinnerling commented 4 years ago

Hi, I'm very enticed by the possibilities of bactMAP and tried to use for analysis of data from MicrobeJ. Just wanted to ask if you had found the time to take a look at this and found a solution? I'm running the development version on R 4.0.2 but the import of seperate contour and maxima CSVs still throws an error, which traces back to mergeframes().

vrrenske commented 4 years ago

Hi! I'll have a look at it and try to resolve it this week! If you have an example where this happens then it would be great if you can send me the CSV files so I can see if something is different from the test files I used.

vrrenske commented 4 years ago

Hi! With the datasets I have, I am not getting this error anymore (R 4.0.2, with contour & maxima CSVs). There might be some differences between our CSVs, if you could send me some example files that would be great, either due to different microbeJ versions or something else. I'd like to improve the compatibility! cheers, Renske

Bwinnerling commented 4 years ago

Hi,

thanks for your reply! I'm sorry I didn't get back to you sooner.

I just tried it again and got the same error as before. I am using MicrobeJ 5.13l on Fiji and R 4.02. I ran the bacteria and maxima detection and exported the CSVs of the results following the instructions from the bactMAP page. I will attach the CSVs I got. I am still quite new to R so it might be that there's a really easy fix for my problem which I just didn't see. The error I get is:

dataloc <- file.choose() spotloc <- file.choose() micdata <- extr_MicrobeJ(dataloc, spotloc, mag = "Staph") Using pixel to micron conversion factor Staph to convert cell contour pixel coordinates to microns. Using pixel to micron conversion factor Staph to convert spot coordinates to microns. Using pixel to micron conversion factor Staph to convert object contour pixel coordinates to microns. Joining, by = "NAME.id" BactMAP detected that the contour (mesh) coordinates are in micron while the maxima (spots) coordinates are in pixels and corrects this. To override, include the command 'keeprealvalues=TRUE' in the extr_MicrobeJ function call. =========================================================================================================================Fehler in $<-.data.frame(*tmp*, "spot", value = 1) : replacement has 1 row, data has 0 traceback() 6: stop(sprintf(ngettext(N, "replacement has %d row, data has %d", "replacement has %d rows, data has %d"), N, nrows), domain = NA) 5: $<-.data.frame(*tmp*, "spot", value = 1) 4: $<-(*tmp*, "spot", value = 1) 3: spotMR(MR) 2: mergeframes(listbox$spots_relative, listbox$mesh, mags) 1: extr_MicrobeJ(dataloc, spotloc, mag = "Staph")

Again, thanks very much for your willingness to help and your supportive feedback.

All the best, Benjamin Winnerling

Am Di., 4. Aug. 2020 um 12:22 Uhr schrieb Renske van Raaphorst < notifications@github.com>:

Hi! With the datasets I have, I am not getting this error anymore (R 4.0.2, with contour & maxima CSVs). There might be some differences between our CSVs, if you could send :renske.vanraaphorst@uclouvain.be me some example files that would be great, either due to different microbeJ versions or something else. I'd like to improve the compatibility! cheers, Renske

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vrrenske commented 4 years ago

Hi Benjamin, I am not sure if this is the problem, but I found that the instructions on the wiki were not up to date. I updated it with extra instructions. Maybe you can see if there are any differences with what you did: https://github.com/veeninglab/BactMAP/wiki/extr_MicrobeJ. If there are still problems, please let me know, I'd be happy to find out what's going on! best wishes, Renske