cytomining / cytominergallery Goto Github PK
View Code? Open in Web Editor NEWA Gallery of Cytominer Vignettes
Home Page: https://cytomining.github.io/cytominergallery/
License: Other
A Gallery of Cytominer Vignettes
Home Page: https://cytomining.github.io/cytominergallery/
License: Other
vignettes/feature_distribution_analysis.Rmd
Hi!
First of all than you for this wonderful set of tools. This absolutely moves the field miles ahead in ability of new people to get up and going on image analysis.
One things that I found myself needing is a way to replicate your work in the paper. The dataset you provide for training is comprised of 14K cells, rather than the one of 150K from the paper. As well there are many great visualizations you accomplish in the paper that are not shown in some of the vignettes (like heatmaps of pairwise comparisons or heatmaps of plate setup), which can be VERY useful to start with. If you could provide the workflow from the paper with the original dataset, that would be absolutely wonderful!
Thank you!
-Elias
Revert #48
Daniel suggested that
"As for the code of the covariance, I have been reading the code and it seems
correct to me. The only comments I would have are the following:
Variable n (declared in line 6) is redundant because inside the loop it has
the same value as "i", and outside the loop (lines 22 and 25) has the same
value as "size".
Checking the size in functions "online_covar" and "two_pass_covar" could be
done before the loop. That way, for size=1 the loop wouldn't execute, saving
a few cycles. However the performance impact of this is very small, I don't
think there is any problem as long as these functions are not called
intensively with 1-length vectors (e.g. as base case for a recursive
function).
I would think comparing the result with that obtained by the R function is
indeed sufficient. Maybe another test would be passing a very large matrix
with some wildly different values in it (to facilitate numeric unstability)
but with known covariances. However I suspect the size would have to be VERY
large to cause problems to the R implementation too."
vignettes/feature_distribution_analysis.Rmd
Possibly remove outliers first?
vignettes/feature_distribution_analysis.Rmd
installation in R 3.3.2 using
devtools::install_github("cytomining/cytominergallery", dependencies = TRUE, build_vignettes = TRUE)
fails with the following error log.
Error: processing vignette 'single_cell_analysis.Rmd' failed with diagnostics:
Path does not exist and create = FALSE
In addition: Warning message:
In tools::buildVignettes(dir = ".", tangle = TRUE) :
Files named as vignettes but with no recognized vignette engine:
‘vignettes/feature_distribution_analysis.Rmd’
(Is a VignetteBuilder field missing?)
Execution halted
Error: Command failed (1)
Comment from Shantanu:
Ah that was because we didn't intend for that to be a vignette but
rather a notebook, but somehow overlooked the fact that
install.packages() will try to build it.
cloned issue from cytomining/cytominer#49
sources: similarity network fusion
http://www.nature.com/nmeth/journal/v11/n3/full/nmeth.2810.html
R implementation
https://github.com/maxconway/SNFtool/blob/master/R/SNF.R
Dependencies in http://r-pkgs.had.co.nz/description.html#dependencies
vignettes/feature_distribution_analysis.Rmd
The current way is working on >95% of cases but there are cases that merging on "ObjectNumber" won't work. @shntnu can you elaborate?
The link to the SQLite db dataset file for vignette single_cell_analysis is dead.
Regards,
Ben
Install using
devtools::install_github("cytomining/cytominergallery", dependencies = TRUE, build_vignettes = TRUE)
fails with
Quitting from lines 47-63 (single_cell_analysis.Rmd)
Error: processing vignette 'single_cell_analysis.Rmd' failed with diagnostics:
Path does not exist and create = FALSE
Execution halted
Error: Command failed (1)
vignettes/feature_distribution_analysis.Rmd
vignettes/feature_distribution_analysis.Rmd
robustbase::mc
http://svitsrv25.epfl.ch/R-doc/library/robustbase/html/mc.html has a different scale from skewness
and so the is_skewed
threshold should be changed.
A declarative, efficient, and flexible JavaScript library for building user interfaces.
🖖 Vue.js is a progressive, incrementally-adoptable JavaScript framework for building UI on the web.
TypeScript is a superset of JavaScript that compiles to clean JavaScript output.
An Open Source Machine Learning Framework for Everyone
The Web framework for perfectionists with deadlines.
A PHP framework for web artisans
Bring data to life with SVG, Canvas and HTML. 📊📈🎉
JavaScript (JS) is a lightweight interpreted programming language with first-class functions.
Some thing interesting about web. New door for the world.
A server is a program made to process requests and deliver data to clients.
Machine learning is a way of modeling and interpreting data that allows a piece of software to respond intelligently.
Some thing interesting about visualization, use data art
Some thing interesting about game, make everyone happy.
We are working to build community through open source technology. NB: members must have two-factor auth.
Open source projects and samples from Microsoft.
Google ❤️ Open Source for everyone.
Alibaba Open Source for everyone
Data-Driven Documents codes.
China tencent open source team.