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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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spotsInBox not working #11

Open vrrenske opened 4 years ago

vrrenske commented 4 years ago

The function which connects spot (fluorescence) data to mesh (segmentation) data from 2 different sources, is giving out an error. This can cause errors in:

spotsInBox() objectsInBox() createPlotList()

I am working on the resolution of this at the moment and will keep you updated.

vrrenske commented 4 years ago

The issue is now resolved in the development version of BactMAP. Please use 

remotes::install_github("vrrenske/bactmap")

to install bactMAP until the next update if you want to use this functionality.

0Bernhard commented 4 years ago

Hello

I downloaded it from your repository but i am still getting an error. Is this something somone else has seen?

thank you

plots_Bacillus <- createPlotList(spotdata=spots_Bacillus$spotframe,

  • meshdata=mesh_Bacillus$mesh,
  • groups=5) Did not find cell data in spot dataset. Running spotsInBox to connect spots to meshes... Package 'SDMTools' needed for this function to work. Press 'y' to install, or any other key to cancel.y Installing package into ‘C:/Users/Berni/Documents/R/win-library/3.6’ (as ‘lib’ is unspecified) =======Error in loadNamespace(name) : there is no package called ‘SDMTools’ In addition: Warning message: package ‘SDMTools’ is not available (for R version 3.6.3)
vrrenske commented 4 years ago

Hi! I will double check this week. The package SDMTools is deprecated in the latest function of CRAN. I thought I replaced the SDMTools functions completely in the version of my repository - but it looks like I missed one function. I will keep you posted!

vrrenske commented 4 years ago

I forgot to update that now it is resolved in the development version on my repository (vrrenske/bactmap). I am working on an update of the "stable" version this week that has all the bug fixes of the last months.