shmohammadi86 / actionet Goto Github PK

View Code? Open in Web Editor NEW

34.0 6.0 7.0 306.11 MB

ACTIONet single-cell analysis framework

actionet's Introduction

ACTIONet R Package

See ACTIONet-R for more information about installing/using ACTIONet R package

ACTIONet Python Package

See ACTIONet-Python for more information about installing/using ACTIONet Python package

How to get more help and file bug reports

Please file a github issue if you are having trouble using ACTIONet or you think you've found a bug.

For more realtime interactive help with a human developer, we encourage you to join the ACTIONet slack workspace:

https://actionet.herokuapp.com/ You can enter your email address, and this will add you to the project's slack workspace (actionetgroup.slack.com)

If you are stuck and need help using actionet, please post to the "help-me" channel.
If you'd like to discuss a bug report, file a github issue, or post on "bugs" channel.

actionet's People

Contributors

Stargazers

Watchers

Forkers

maheshjethalia abuchin annashch-insitro chenatf vonwillie ricomnl maarten-devries

actionet's Issues

Detailed documentation required

I am getting to know the package and I find the potential is very high for these kind of packages. I would like to use it in combination with SCINET. However, there is some contradicting information between the docs of ACTION and the demo's situated in the SCINET repo. In general I had the following question:

Are the ace$S_r and ace$ACTION attribute the same? Do they represent the ACTION similarity metric/kernel?
Why does ace$ACTION have a dim of n_cells x reduced_dim instead of n_cells x n_cells like the ace$ACTIONet?
What is the difference between the attributes Enrichment and Confidence after annotating the archetypes?
In the ACTION docs, unreliable archetypes are pruned and unified manually while this seems to be done automatically in the SCINET demo? Was this an update and is this now always done automatically?
There is no ace$trace attribute
I can't find the function update.Labels
From the ACTION docs it seems that you need the build the ACTION graph yourself with build_ACTIONet and then store is under ace$ACTIONet, but by default after running ACTIONet there is already an attribute containing a matrix of n_cells x n_cells which I assume holds cell similarity values between 0 and 1?
In the SCINET demo they use a function plot.ACTIONet.igraph but I can't find that function. Has it been deprecated in favor of plot.ACTIONet?
Is there a way to specify upfront how many archetypes you want?

I realize this is a lot to ask for but I would greatly appreciate of you could help me this!

Thanks a lot!

R package loading/linking error

I am trying to install the ACTIONet R package on an Ubuntu 16.04 system (that is the version of the computers on our cluster). I have to use a newer version of gcc than the one standard for 16.04, so I am using an install of gcc 8.2.0. Basically, when trying to load the ACTIONet.so file, it looks for the libstdc++ library. However, the library file that it finds is the wrong one.... it needs to find the one associated with the install of gcc 8.2.0, NOT the default one. I have set all of the environment variables I can think of, such as LD_LIBRARY_PATH, LIBRARY_PATH, C_INCLUDE_PATH, etc. to point to the correct directory (/software/gcc/8.2.0/lssc0-linux/lib64), and yet I am still getting the problem below. I have also tried adding the path as a "-L" option in the Makevars file, but still the same error.

So for the testing of loading from the temp location... does that somehow not get the correct path? Any help would be highly appreciated.

** testing if installed package can be loaded from temporary location
Warning: replacing previous import 'ggplot2::last_plot' by 'plotly::last_plot' when loading 'ACTIONet'
Error: package or namespace load failed for 'ACTIONet' in dyn.load(file, DLLpath = DLLpath, ...):
unable to load shared object '/share/biocore/joshi/sandbox/actionet/00LOCK-ACTIONet/00new/ACTIONet/libs/ACTIONet.so':
/usr/lib/x86_64-linux-gnu/libstdc++.so.6: version `GLIBCXX_3.4.22' not found (required by /share/biocore/joshi/sandbox/actionet/00LOCK-ACTIONet/00new/ACTIONet/libs/ACTIONet.so)
Error: loading failed
Execution halted
ERROR: loading failed
* removing '/share/biocore/joshi/sandbox/actionet/ACTIONet'

Annotation using markers

For both annotate.archetypes.using.markers and annotate.cells.using.markers, a list of lists of genes are provided, each list specifying gene markers for a cell type.

When there aren't cell names assigned to the lists, we give them generic Celltype %s names, where %s is 1...# of cells.
I don't think these names are applied to the marker genes list at all.
https://github.com/shmohammadi86/ACTIONet/blob/R-devel/R/annotation.R#L101
https://github.com/shmohammadi86/ACTIONet/blob/R-devel/R/annotation.R#L210

Therefore, when creating the markers.table, names(marker.genes) == NULL and the markers.table is empty.
Not familiar with R conventions of doing this, so posting an issue instead.

Error in ACTIONet:::.preprocess_marker_labels

Hi,

When trying to annotate cell types using markers I get the following error:
Error in ACTIONet:::.preprocess_marker_labels(markers, rownames(S)) : object 'markers' not found

My command:
annot.out = annotate.cells.using.markers(ace = ACTIONet.out, markers = marker.genes, thread_no = 12)

It seems that the preprocessing function can't find the markers object even though it is a required argument. Also, when I leave out the markers argument I get the same error instead of an error pointing to a missing argument with no default (like with ace).

What could be the problem here?

Kind regards

Can't install anymore

Hi,

I can't install the package anymore. I tried building a docker image from the Dockerfile you have in the repository. Here's part of the log:

 building ‘ACTIONetExperiment_1.0.2.tar.gz’

Installing package into ‘/usr/local/lib/R/site-library’
(as ‘lib’ is unspecified)
* installing *source* package ‘ACTIONetExperiment’ ...
** using staged installation
** libs
g++ -std=gnu++14 -I"/usr/local/lib/R/include" -DNDEBUG `find ../inst/include -type d -print | sed s/^/-I/` -w -m64 -DINT_64BITS -DARMA_64BIT_WORD -O3 -w -m64 -
fno-strict-aliasing -fomit-frame-pointer -funroll-loops -fexpensive-optimizations -I'/usr/local/lib/R/site-library/Rcpp/include' -I'/usr/local/lib/R/site-libra
ry/RcppArmadillo/include' -I/usr/local/include  `find ../inst/include -type d -print | sed s/^/-I/` -w -m64 -DINT_64BITS -DARMA_64BIT_WORD -O3 -w -std=c++14 -m
64 -fno-strict-aliasing -fomit-frame-pointer -funroll-loops -fexpensive-optimizations -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -
Wdate-time -D_FORTIFY_SOURCE=2 -g  -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++14 -I"/usr/local/lib/R/include" -DNDEBUG `find ../inst/include -type d -print | sed s/^/-I/` -w -m64 -DINT_64BITS -DARMA_64BIT_WORD -O3 -w -m64 -
fno-strict-aliasing -fomit-frame-pointer -funroll-loops -fexpensive-optimizations -I'/usr/local/lib/R/site-library/Rcpp/include' -I'/usr/local/lib/R/site-libra
ry/RcppArmadillo/include' -I/usr/local/include  `find ../inst/include -type d -print | sed s/^/-I/` -w -m64 -DINT_64BITS -DARMA_64BIT_WORD -O3 -w -std=c++14 -m
64 -fno-strict-aliasing -fomit-frame-pointer -funroll-loops -fexpensive-optimizations -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -
Wdate-time -D_FORTIFY_SOURCE=2 -g  -c RCpp_util.cpp -o RCpp_util.o
g++ -std=gnu++14 -shared -L/usr/local/lib/R/lib -L/usr/local/lib -o ACTIONetExperiment.so RcppExports.o RCpp_util.o -L/usr/local/lib/R/lib -lR
installing to /usr/local/lib/R/site-library/00LOCK-ACTIONetExperiment/00new/ACTIONetExperiment/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (ACTIONetExperiment)
Downloading GitHub repo shmohammadi86/ACTIONet@R-release
'/usr/bin/git' clone --depth 1 --no-hardlinks --recurse-submodules --branch core https://github.com/shmohammadi86/ACTIONet.git /tmp/Rtmphc8IaJ/remotes25d77cd02
/shmohammadi86-ACTIONet-a14d783/src/ACTIONet
Cloning into '/tmp/Rtmphc8IaJ/remotes25d77cd02/shmohammadi86-ACTIONet-a14d783/src/ACTIONet'...
── R CMD build ─────────────────────────────────────────────────────────────────
* checking for file ‘/tmp/Rtmphc8IaJ/remotes25d77cd02/shmohammadi86-ACTIONet-a14d783/DESCRIPTION’ ... OK
* preparing ‘ACTIONet’:
* checking DESCRIPTION meta-information ... OK
* cleaning src
* checking for LF line-endings in source and make files and shell scripts
* checking for empty or unneeded directories
* looking to see if a ‘data/datalist’ file should be added
* building ‘ACTIONet_3.0.1.tar.gz’

Installing package into ‘/usr/local/lib/R/site-library’
(as ‘lib’ is unspecified)
* installing *source* package ‘ACTIONet’ ...
** using staged installation
** libs
Using Linux configurations
g++ -std=gnu++14 -I"/usr/local/lib/R/include" -DNDEBUG `find /tmp/RtmpVmxLbv/R.INSTALLfc8fb1874/ACTIONet/src/ACTIONet/include -type d -print | sed s/^/-I/` -I.
./inst/include -w -m64 -DINT_64BITS -DARMA_64BIT_WORD -O3 -w -m64 -fno-strict-aliasing -fomit-frame-pointer -funroll-loops -I/usr/include/suitesparse -I'/usr/l
ocal/lib/R/site-library/Rcpp/include' -I'/usr/local/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include  `find /tmp/RtmpVmxLbv/R.INSTALLfc8fb1874/AC
TIONet/src/ACTIONet/include -type d -print | sed s/^/-I/` -I../inst/include -w -m64 -DINT_64BITS -DARMA_64BIT_WORD -O3 -w -std=c++14 -m64 -fno-strict-aliasing 
-fomit-frame-pointer -funroll-loops -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c ACTIONet/src
/misc/HDBSCAN/hdbscanAlgorithm.cc -o ACTIONet/src/misc/HDBSCAN/hdbscanAlgorithm.o
g++ -std=gnu++14 -I"/usr/local/lib/R/include" -DNDEBUG `find /tmp/RtmpVmxLbv/R.INSTALLfc8fb1874/ACTIONet/src/ACTIONet/include -type d -print | sed s/^/-I/` -I.
./inst/include -w -m64 -DINT_64BITS -DARMA_64BIT_WORD -O3 -w -m64 -fno-strict-aliasing -fomit-frame-pointer -funroll-loops -I/usr/include/suitesparse -I'/usr/l
ocal/lib/R/site-library/Rcpp/include' -I'/usr/local/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include  `find /tmp/RtmpVmxLbv/R.INSTALLfc8fb1874/AC
TIONet/src/ACTIONet/include -type d -print | sed s/^/-I/` -I../inst/include -w -m64 -DINT_64BITS -DARMA_64BIT_WORD -O3 -w -std=c++14 -m64 -fno-strict-aliasing 
-fomit-frame-pointer -funroll-loops -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c ACTIONet/src
/misc/HDBSCAN/ManhattanDistance.cc -o ACTIONet/src/misc/HDBSCAN/ManhattanDistance.o
g++ -std=gnu++14 -I"/usr/local/lib/R/include" -DNDEBUG `find /tmp/RtmpVmxLbv/R.INSTALLfc8fb1874/ACTIONet/src/ACTIONet/include -type d -print | sed s/^/-I/` -I.
./inst/include -w -m64 -DINT_64BITS -DARMA_64BIT_WORD -O3 -w -m64 -fno-strict-aliasing -fomit-frame-pointer -funroll-loops -I/usr/include/suitesparse -I'/usr/l
ocal/lib/R/site-library/Rcpp/include' -I'/usr/local/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include  `find /tmp/RtmpVmxLbv/R.INSTALLfc8fb1874/AC
TIONet/src/ACTIONet/include -type d -print | sed s/^/-I/` -I../inst/include -w -m64 -DINT_64BITS -DARMA_64BIT_WORD -O3 -w -std=c++14 -m64 -fno-strict-aliasing 
-fomit-frame-pointer -funroll-loops -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c ACTIONet/src
/misc/HDBSCAN/hdbscanConstraint.cc -o ACTIONet/src/misc/HDBSCAN/hdbscanConstraint.o
g++ -std=gnu++14 -I"/usr/local/lib/R/include" -DNDEBUG `find /tmp/RtmpVmxLbv/R.INSTALLfc8fb1874/ACTIONet/src/ACTIONet/include -type d -print | sed s/^/-I/` -I.
./inst/include -w -m64 -DINT_64BITS -DARMA_64BIT_WORD -O3 -w -m64 -fno-strict-aliasing -fomit-frame-pointer -funroll-loops -I/usr/include/suitesparse -I'/usr/l
ocal/lib/R/site-library/Rcpp/include' -I'/usr/local/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include  `find /tmp/RtmpVmxLbv/R.INSTALLfc8fb1874/AC
TIONet/src/ACTIONet/include -type d -print | sed s/^/-I/` -I../inst/include -w -m64 -DINT_64BITS -DARMA_64BIT_WORD -O3 -w -std=c++14 -m64 -fno-strict-aliasing 
-fomit-frame-pointer -funroll-loops -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c ACTIONet/src
/misc/HDBSCAN/outlierScore.cc -o ACTIONet/src/misc/HDBSCAN/outlierScore.o
g++ -std=gnu++14 -I"/usr/local/lib/R/include" -DNDEBUG `find /tmp/RtmpVmxLbv/R.INSTALLfc8fb1874/ACTIONet/src/ACTIONet/include -type d -print | sed s/^/-I/` -I.
./inst/include -w -m64 -DINT_64BITS -DARMA_64BIT_WORD -O3 -w -m64 -fno-strict-aliasing -fomit-frame-pointer -funroll-loops -I/usr/include/suitesparse -I'/usr/l
ocal/lib/R/site-library/Rcpp/include' -I'/usr/local/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include  `find /tmp/RtmpVmxLbv/R.INSTALLfc8fb1874/AC
TIONet/src/ACTIONet/include -type d -print | sed s/^/-I/` -I../inst/include -w -m64 -DINT_64BITS -DARMA_64BIT_WORD -O3 -w -std=c++14 -m64 -fno-strict-aliasing 
-fomit-frame-pointer -funroll-loops -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c ACTIONet/src
/misc/HDBSCAN/undirectedGraph.cc -o ACTIONet/src/misc/HDBSCAN/undirectedGraph.o
g++ -std=gnu++14 -I"/usr/local/lib/R/include" -DNDEBUG `find /tmp/RtmpVmxLbv/R.INSTALLfc8fb1874/ACTIONet/src/ACTIONet/include -type d -print | sed s/^/-I/` -I.
./inst/include -w -m64 -DINT_64BITS -DARMA_64BIT_WORD -O3 -w -m64 -fno-strict-aliasing -fomit-frame-pointer -funroll-loops -I/usr/include/suitesparse -I'/usr/l
ocal/lib/R/site-library/Rcpp/include' -I'/usr/local/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include  `find /tmp/RtmpVmxLbv/R.INSTALLfc8fb1874/AC
TIONet/src/ACTIONet/include -type d -print | sed s/^/-I/` -I../inst/include -w -m64 -DINT_64BITS -DARMA_64BIT_WORD -O3 -w -std=c++14 -m64 -fno-strict-aliasing 
-fomit-frame-pointer -funroll-loops -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c ACTIONet/src
/misc/HDBSCAN/cluster.cc -o ACTIONet/src/misc/HDBSCAN/cluster.o
g++ -std=gnu++14 -I"/usr/local/lib/R/include" -DNDEBUG `find /tmp/RtmpVmxLbv/R.INSTALLfc8fb1874/ACTIONet/src/ACTIONet/include -type d -print | sed s/^/-I/` -I.
./inst/include -w -m64 -DINT_64BITS -DARMA_64BIT_WORD -O3 -w -m64 -fno-strict-aliasing -fomit-frame-pointer -funroll-loops -I/usr/include/suitesparse -I'/usr/l
ocal/lib/R/site-library/Rcpp/include' -I'/usr/local/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include  `find /tmp/RtmpVmxLbv/R.INSTALLfc8fb1874/AC
TIONet/src/ACTIONet/include -type d -print | sed s/^/-I/` -I../inst/include -w -m64 -DINT_64BITS -DARMA_64BIT_WORD -O3 -w -std=c++14 -m64 -fno-strict-aliasing 
-fomit-frame-pointer -funroll-loops -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c ACTIONet/src
/misc/HDBSCAN/hdbscan.cc -o ACTIONet/src/misc/HDBSCAN/hdbscan.o
g++ -std=gnu++14 -I"/usr/local/lib/R/include" -DNDEBUG `find /tmp/RtmpVmxLbv/R.INSTALLfc8fb1874/ACTIONet/src/ACTIONet/include -type d -print | sed s/^/-I/` -I.
./inst/include -w -m64 -DINT_64BITS -DARMA_64BIT_WORD -O3 -w -m64 -fno-strict-aliasing -fomit-frame-pointer -funroll-loops -I/usr/include/suitesparse -I'/usr/l
ocal/lib/R/site-library/Rcpp/include' -I'/usr/local/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include  `find /tmp/RtmpVmxLbv/R.INSTALLfc8fb1874/AC
TIONet/src/ACTIONet/include -type d -print | sed s/^/-I/` -I../inst/include -w -m64 -DINT_64BITS -DARMA_64BIT_WORD -O3 -w -std=c++14 -m64 -fno-strict-aliasing 
-fomit-frame-pointer -funroll-loops -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c ACTIONet/src
/misc/HDBSCAN/bitSet.cc -o ACTIONet/src/misc/HDBSCAN/bitSet.o
g++ -std=gnu++14 -I"/usr/local/lib/R/include" -DNDEBUG `find /tmp/RtmpVmxLbv/R.INSTALLfc8fb1874/ACTIONet/src/ACTIONet/include -type d -print | sed s/^/-I/` -I.
./inst/include -w -m64 -DINT_64BITS -DARMA_64BIT_WORD -O3 -w -m64 -fno-strict-aliasing -fomit-frame-pointer -funroll-loops -I/usr/include/suitesparse -I'/usr/l
ocal/lib/R/site-library/Rcpp/include' -I'/usr/local/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include  `find /tmp/RtmpVmxLbv/R.INSTALLfc8fb1874/AC
TIONet/src/ACTIONet/include -type d -print | sed s/^/-I/` -I../inst/include -w -m64 -DINT_64BITS -DARMA_64BIT_WORD -O3 -w -std=c++14 -m64 -fno-strict-aliasing 
-fomit-frame-pointer -funroll-loops -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c ACTIONet/src
/misc/HDBSCAN/hdbscanRunner.cc -o ACTIONet/src/misc/HDBSCAN/hdbscanRunner.o
In file included from /tmp/RtmpVmxLbv/R.INSTALLfc8fb1874/ACTIONet/src/ACTIONet/include/arma/armadillo_bits/Mat_meat.hpp:9921,
                 from /tmp/RtmpVmxLbv/R.INSTALLfc8fb1874/ACTIONet/src/ACTIONet/include/arma/armadillo:616,
                 from /usr/local/lib/R/site-library/RcppArmadillo/include/RcppArmadillo/interface/RcppArmadilloForward.h:56,
                 from /usr/local/lib/R/site-library/RcppArmadillo/include/RcppArmadillo.h:29,
                 from ../inst/include/ACTIONet.h:13,
                 from /tmp/RtmpVmxLbv/R.INSTALLfc8fb1874/ACTIONet/src/ACTIONet/include/clustering/HDBSCAN/hdbscan.hpp:2,
                 from ACTIONet/src/misc/HDBSCAN/hdbscan.cc:1:
/usr/local/lib/R/site-library/RcppArmadillo/include/RcppArmadillo/internal/Mat_meat.h: In constructor ‘arma::Mat<eT>::Mat(const Rcpp::VectorBase<RTYPE, NA, VEC
TOR>&)’:
/usr/local/lib/R/site-library/RcppArmadillo/include/RcppArmadillo/internal/Mat_meat.h:104:11: error: class ‘arma::Mat<eT>’ does not have any field named ‘n_all
oc’
  104 |         , n_alloc(0)
      |           ^~~~~~~
/usr/local/lib/R/site-library/RcppArmadillo/include/RcppArmadillo/internal/Mat_meat.h: In constructor ‘arma::Mat<eT>::Mat(const Rcpp::MatrixBase<RTYPE, NA, VEC
TOR>&)’:
/usr/local/lib/R/site-library/RcppArmadillo/include/RcppArmadillo/internal/Mat_meat.h:124:11: error: class ‘arma::Mat<eT>’ does not have any field named ‘n_all
oc’
  124 |         , n_alloc(0)
      |           ^~~~~~~
In file included from /usr/local/lib/R/site-library/RcppArmadillo/include/RcppArmadillo.h:29,
                 from ../inst/include/ACTIONet.h:13,
                 from /tmp/RtmpVmxLbv/R.INSTALLfc8fb1874/ACTIONet/src/ACTIONet/include/clustering/HDBSCAN/hdbscan.hpp:2,
                 from ACTIONet/src/misc/HDBSCAN/hdbscan.cc:1:
/usr/local/lib/R/site-library/RcppArmadillo/include/RcppArmadillo/interface/RcppArmadilloForward.h: At global scope:
/usr/local/lib/R/site-library/RcppArmadillo/include/RcppArmadillo/interface/RcppArmadilloForward.h:67:51: error: ‘subview_cols’ in namespace ‘arma’ does not na
me a template type; did you mean ‘subview_col’?
   67 |     template <typename T> SEXP wrap ( const arma::subview_cols<T>& ) ;
      |                                                   ^~~~~~~~~~~~
      |                                                   subview_col
/usr/local/lib/R/site-library/RcppArmadillo/include/RcppArmadillo/interface/RcppArmadilloForward.h:67:63: error: expected ‘,’ or ‘...’ before ‘<’ token
   67 |     template <typename T> SEXP wrap ( const arma::subview_cols<T>& ) ;
      |                                                               ^
g++ -std=gnu++14 -I"/usr/local/lib/R/include" -DNDEBUG `find /tmp/RtmpVmxLbv/R.INSTALLfc8fb1874/ACTIONet/src/ACTIONet/include -type d -print | sed s/^/-I/` -I.
./inst/include -w -m64 -DINT_64BITS -DARMA_64BIT_WORD -O3 -w -m64 -fno-strict-aliasing -fomit-frame-pointer -funroll-loops -I/usr/include/suitesparse -I'/usr/l
ocal/lib/R/site-library/Rcpp/include' -I'/usr/local/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include  `find /tmp/RtmpVmxLbv/R.INSTALLfc8fb1874/AC
TIONet/src/ACTIONet/include -type d -print | sed s/^/-I/` -I../inst/include -w -m64 -DINT_64BITS -DARMA_64BIT_WORD -O3 -w -std=c++14 -m64 -fno-strict-aliasing 
-fomit-frame-pointer -funroll-loops -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c ACTIONet/src
/misc/HDBSCAN/hdbscanParameters.cc -o ACTIONet/src/misc/HDBSCAN/hdbscanParameters.o
g++ -std=gnu++14 -I"/usr/local/lib/R/include" -DNDEBUG `find /tmp/RtmpVmxLbv/R.INSTALLfc8fb1874/ACTIONet/src/ACTIONet/include -type d -print | sed s/^/-I/` -I.
./inst/include -w -m64 -DINT_64BITS -DARMA_64BIT_WORD -O3 -w -m64 -fno-strict-aliasing -fomit-frame-pointer -funroll-loops -I/usr/include/suitesparse -I'/usr/l
ocal/lib/R/site-library/Rcpp/include' -I'/usr/local/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include  `find /tmp/RtmpVmxLbv/R.INSTALLfc8fb1874/AC
TIONet/src/ACTIONet/include -type d -print | sed s/^/-I/` -I../inst/include -w -m64 -DINT_64BITS -DARMA_64BIT_WORD -O3 -w -std=c++14 -m64 -fno-strict-aliasing 
-fomit-frame-pointer -funroll-loops -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c ACTIONet/src
/misc/HDBSCAN/EuclideanDistance.cc -o ACTIONet/src/misc/HDBSCAN/EuclideanDistance.o
g++ -std=gnu++14 -I"/usr/local/lib/R/include" -DNDEBUG `find /tmp/RtmpVmxLbv/R.INSTALLfc8fb1874/ACTIONet/src/ACTIONet/include -type d -print | sed s/^/-I/` -I.
./inst/include -w -m64 -DINT_64BITS -DARMA_64BIT_WORD -O3 -w -m64 -fno-strict-aliasing -fomit-frame-pointer -funroll-loops -I/usr/include/suitesparse -I'/usr/l
ocal/lib/R/site-library/Rcpp/include' -I'/usr/local/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include  `find /tmp/RtmpVmxLbv/R.INSTALLfc8fb1874/AC
TIONet/src/ACTIONet/include -type d -print | sed s/^/-I/` -I../inst/include -w -m64 -DINT_64BITS -DARMA_64BIT_WORD -O3 -w -std=c++14 -m64 -fno-strict-aliasing 
-fomit-frame-pointer -funroll-loops -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c ACTIONet/src
/misc/HDBSCAN/hdbscanResult.cc -o ACTIONet/src/misc/HDBSCAN/hdbscanResult.o
g++ -std=gnu++14 -I"/usr/local/lib/R/include" -DNDEBUG `find /tmp/RtmpVmxLbv/R.INSTALLfc8fb1874/ACTIONet/src/ACTIONet/include -type d -print | sed s/^/-I/` -I.
./inst/include -w -m64 -DINT_64BITS -DARMA_64BIT_WORD -O3 -w -m64 -fno-strict-aliasing -fomit-frame-pointer -funroll-loops -I/usr/include/suitesparse -I'/usr/l
ocal/lib/R/site-library/Rcpp/include' -I'/usr/local/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include  `find /tmp/RtmpVmxLbv/R.INSTALLfc8fb1874/AC
TIONet/src/ACTIONet/include -type d -print | sed s/^/-I/` -I../inst/include -w -m64 -DINT_64BITS -DARMA_64BIT_WORD -O3 -w -std=c++14 -m64 -fno-strict-aliasing 
-fomit-frame-pointer -funroll-loops -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c ACTIONet/src
/misc/HDBSCAN/IDistanceCalculator.cc -o ACTIONet/src/misc/HDBSCAN/IDistanceCalculator.o
g++ -std=gnu++14 -I"/usr/local/lib/R/include" -DNDEBUG `find /tmp/RtmpVmxLbv/R.INSTALLfc8fb1874/ACTIONet/src/ACTIONet/include -type d -print | sed s/^/-I/` -I.
./inst/include -w -m64 -DINT_64BITS -DARMA_64BIT_WORD -O3 -w -m64 -fno-strict-aliasing -fomit-frame-pointer -funroll-loops -I/usr/include/suitesparse -I'/usr/l
ocal/lib/R/site-library/Rcpp/include' -I'/usr/local/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include  `find /tmp/RtmpVmxLbv/R.INSTALLfc8fb1874/AC
TIONet/src/ACTIONet/include -type d -print | sed s/^/-I/` -I../inst/include -w -m64 -DINT_64BITS -DARMA_64BIT_WORD -O3 -w -std=c++14 -m64 -fno-strict-aliasing 
-fomit-frame-pointer -funroll-loops -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c ACTIONet/src
/misc/my_utils.cc -o ACTIONet/src/misc/my_utils.o
In file included from /usr/local/lib/R/site-library/RcppArmadillo/include/RcppArmadillo.h:35,
                 from ../inst/include/ACTIONet.h:13,
                 from /tmp/RtmpVmxLbv/R.INSTALLfc8fb1874/ACTIONet/src/ACTIONet/include/clustering/HDBSCAN/hdbscan.hpp:2,
                 from ACTIONet/src/misc/HDBSCAN/hdbscan.cc:1:
/usr/local/lib/R/site-library/RcppArmadillo/include/RcppArmadillo/interface/RcppArmadilloWrap.h:57:45: error: ‘subview_cols’ in namespace ‘arma’ does not name 
a template type; did you mean ‘subview_col’?
   57 |         SEXP arma_subview_wrap( const arma::subview_cols<T>& data, int nrows, int ncols ){
      |                                             ^~~~~~~~~~~~
      |                                             subview_col
/usr/local/lib/R/site-library/RcppArmadillo/include/RcppArmadillo/interface/RcppArmadilloWrap.h:57:57: error: expected ‘,’ or ‘...’ before ‘<’ token
   57 |         SEXP arma_subview_wrap( const arma::subview_cols<T>& data, int nrows, int ncols ){
      |                                                         ^
/usr/local/lib/R/site-library/RcppArmadillo/include/RcppArmadillo/interface/RcppArmadilloWrap.h: In function ‘SEXPREC* Rcpp::RcppArmadillo::arma_subview_wrap(i
nt)’:
/usr/local/lib/R/site-library/RcppArmadillo/include/RcppArmadillo/interface/RcppArmadilloWrap.h:59:38: error: ‘nrows’ was not declared in this scope; did you m
ean ‘row’?
   59 |             Rcpp::Matrix<RTYPE> mat( nrows, ncols ) ;
      |                                      ^~~~~
      |                                      row
/usr/local/lib/R/site-library/RcppArmadillo/include/RcppArmadillo/interface/RcppArmadilloWrap.h:59:45: error: ‘ncols’ was not declared in this scope; did you m
ean ‘cos’?
   59 |             Rcpp::Matrix<RTYPE> mat( nrows, ncols ) ;
      |                                             ^~~~~
      |                                             cos
/usr/local/lib/R/site-library/RcppArmadillo/include/RcppArmadillo/interface/RcppArmadilloWrap.h:61:31: error: ‘data’ was not declared in this scope
   61 |             const T* svcmem = data.colptr(0);
      |                               ^~~~
/usr/local/lib/R/site-library/RcppArmadillo/include/RcppArmadillo/interface/RcppArmadilloWrap.h: At global scope:
/usr/local/lib/R/site-library/RcppArmadillo/include/RcppArmadillo/interface/RcppArmadilloWrap.h:99:50: error: ‘subview_cols’ in namespace ‘arma’ does not name 
a template type; did you mean ‘subview_col’?
   99 |     template <typename T> SEXP wrap( const arma::subview_cols<T>& data ){
      |                                                  ^~~~~~~~~~~~
      |                                                  subview_col
/usr/local/lib/R/site-library/RcppArmadillo/include/RcppArmadillo/interface/RcppArmadilloWrap.h:99:62: error: expected ‘,’ or ‘...’ before ‘<’ token
   99 |     template <typename T> SEXP wrap( const arma::subview_cols<T>& data ){
      |                                                              ^
/usr/local/lib/R/site-library/RcppArmadillo/include/RcppArmadillo/interface/RcppArmadilloWrap.h: In function ‘SEXPREC* Rcpp::wrap(int)’:
/usr/local/lib/R/site-library/RcppArmadillo/include/RcppArmadillo/interface/RcppArmadilloWrap.h:100:53: error: ‘data’ was not declared in this scope
  100 |         return RcppArmadillo::arma_subview_wrap<T>( data, data.n_rows, data.n_cols ) ;
      |                                                     ^~~~
make: *** [/usr/local/lib/R/etc/Makeconf:176: ACTIONet/src/misc/HDBSCAN/hdbscan.o] Error 1
make: *** Waiting for unfinished jobs....
In file included from /tmp/RtmpVmxLbv/R.INSTALLfc8fb1874/ACTIONet/src/ACTIONet/include/arma/armadillo_bits/Mat_meat.hpp:9921,
                 from /tmp/RtmpVmxLbv/R.INSTALLfc8fb1874/ACTIONet/src/ACTIONet/include/arma/armadillo:616,
                 from /usr/local/lib/R/site-library/RcppArmadillo/include/RcppArmadillo/interface/RcppArmadilloForward.h:56,
                 from /usr/local/lib/R/site-library/RcppArmadillo/include/RcppArmadillo.h:29,
                 from ../inst/include/ACTIONet.h:13,
                 from /tmp/RtmpVmxLbv/R.INSTALLfc8fb1874/ACTIONet/src/ACTIONet/include/misc/my_utils.h:4,
                 from ACTIONet/src/misc/my_utils.cc:1:
/usr/local/lib/R/site-library/RcppArmadillo/include/RcppArmadillo/internal/Mat_meat.h: In constructor ‘arma::Mat<eT>::Mat(const Rcpp::VectorBase<RTYPE, NA, VEC
TOR>&)’:
/usr/local/lib/R/site-library/RcppArmadillo/include/RcppArmadillo/internal/Mat_meat.h:104:11: error: class ‘arma::Mat<eT>’ does not have any field named ‘n_all
oc’
  104 |         , n_alloc(0)
      |           ^~~~~~~
/usr/local/lib/R/site-library/RcppArmadillo/include/RcppArmadillo/internal/Mat_meat.h: In constructor ‘arma::Mat<eT>::Mat(const Rcpp::MatrixBase<RTYPE, NA, VEC
TOR>&)’:
/usr/local/lib/R/site-library/RcppArmadillo/include/RcppArmadillo/internal/Mat_meat.h:124:11: error: class ‘arma::Mat<eT>’ does not have any field named ‘n_all
oc’
  124 |         , n_alloc(0)
      |           ^~~~~~~
In file included from /usr/local/lib/R/site-library/RcppArmadillo/include/RcppArmadillo.h:29,
                 from ../inst/include/ACTIONet.h:13,
                 from /tmp/RtmpVmxLbv/R.INSTALLfc8fb1874/ACTIONet/src/ACTIONet/include/misc/my_utils.h:4,
                 from ACTIONet/src/misc/my_utils.cc:1:
/usr/local/lib/R/site-library/RcppArmadillo/include/RcppArmadillo/interface/RcppArmadilloForward.h: At global scope:
/usr/local/lib/R/site-library/RcppArmadillo/include/RcppArmadillo/interface/RcppArmadilloForward.h:67:51: error: ‘subview_cols’ in namespace ‘arma’ does not na
me a template type; did you mean ‘subview_col’?
   67 |     template <typename T> SEXP wrap ( const arma::subview_cols<T>& ) ;
      |                                                   ^~~~~~~~~~~~
      |                                                   subview_col
/usr/local/lib/R/site-library/RcppArmadillo/include/RcppArmadillo/interface/RcppArmadilloForward.h:67:63: error: expected ‘,’ or ‘...’ before ‘<’ token
   67 |     template <typename T> SEXP wrap ( const arma::subview_cols<T>& ) ;
      |                                                               ^
In file included from /usr/local/lib/R/site-library/RcppArmadillo/include/RcppArmadillo.h:35,
                 from ../inst/include/ACTIONet.h:13,
                 from /tmp/RtmpVmxLbv/R.INSTALLfc8fb1874/ACTIONet/src/ACTIONet/include/misc/my_utils.h:4,
                 from ACTIONet/src/misc/my_utils.cc:1:
/usr/local/lib/R/site-library/RcppArmadillo/include/RcppArmadillo/interface/RcppArmadilloWrap.h:57:45: error: ‘subview_cols’ in namespace ‘arma’ does not name 
a template type; did you mean ‘subview_col’?
   57 |         SEXP arma_subview_wrap( const arma::subview_cols<T>& data, int nrows, int ncols ){
      |                                             ^~~~~~~~~~~~
      |                                             subview_col
/usr/local/lib/R/site-library/RcppArmadillo/include/RcppArmadillo/interface/RcppArmadilloWrap.h:57:57: error: expected ‘,’ or ‘...’ before ‘<’ token
   57 |         SEXP arma_subview_wrap( const arma::subview_cols<T>& data, int nrows, int ncols ){
      |                                                         ^
/usr/local/lib/R/site-library/RcppArmadillo/include/RcppArmadillo/interface/RcppArmadilloWrap.h: In function ‘SEXPREC* Rcpp::RcppArmadillo::arma_subview_wrap(i
nt)’:
/usr/local/lib/R/site-library/RcppArmadillo/include/RcppArmadillo/interface/RcppArmadilloWrap.h:59:38: error: ‘nrows’ was not declared in this scope; did you m
ean ‘row’?
   59 |             Rcpp::Matrix<RTYPE> mat( nrows, ncols ) ;
      |                                      ^~~~~
      |                                      row
/usr/local/lib/R/site-library/RcppArmadillo/include/RcppArmadillo/interface/RcppArmadilloWrap.h:59:45: error: ‘ncols’ was not declared in this scope; did you m
ean ‘cos’?
   59 |             Rcpp::Matrix<RTYPE> mat( nrows, ncols ) ;
      |                                             ^~~~~
      |                                             cos
/usr/local/lib/R/site-library/RcppArmadillo/include/RcppArmadillo/interface/RcppArmadilloWrap.h:61:31: error: ‘data’ was not declared in this scope
   61 |             const T* svcmem = data.colptr(0);
      |                               ^~~~
/usr/local/lib/R/site-library/RcppArmadillo/include/RcppArmadillo/interface/RcppArmadilloWrap.h: At global scope:
/usr/local/lib/R/site-library/RcppArmadillo/include/RcppArmadillo/interface/RcppArmadilloWrap.h:99:50: error: ‘subview_cols’ in namespace ‘arma’ does not name 
a template type; did you mean ‘subview_col’?
   99 |     template <typename T> SEXP wrap( const arma::subview_cols<T>& data ){
      |                                                  ^~~~~~~~~~~~
      |                                                  subview_col
/usr/local/lib/R/site-library/RcppArmadillo/include/RcppArmadillo/interface/RcppArmadilloWrap.h:99:62: error: expected ‘,’ or ‘...’ before ‘<’ token
   99 |     template <typename T> SEXP wrap( const arma::subview_cols<T>& data ){
      |                                                              ^
/usr/local/lib/R/site-library/RcppArmadillo/include/RcppArmadillo/interface/RcppArmadilloWrap.h: In function ‘SEXPREC* Rcpp::wrap(int)’:
/usr/local/lib/R/site-library/RcppArmadillo/include/RcppArmadillo/interface/RcppArmadilloWrap.h:100:53: error: ‘data’ was not declared in this scope
  100 |         return RcppArmadillo::arma_subview_wrap<T>( data, data.n_rows, data.n_cols ) ;
      |                                                     ^~~~
make: *** [/usr/local/lib/R/etc/Makeconf:176: ACTIONet/src/misc/my_utils.o] Error 1
ERROR: compilation failed for package ‘ACTIONet’
* removing ‘/usr/local/lib/R/site-library/ACTIONet’
Warning message:
In i.p(...) :
  installation of package ‘/tmp/Rtmphc8IaJ/file229c8f86b/ACTIONet_3.0.1.tar.gz’ had non-zero exit status
--> 8bdc1fca966
STEP 8/8: CMD ["/init"]
COMMIT actionnet_minidocker
--> b2ac55511a4
Successfully tagged localhost/actionnet_minidocker:latest

Installing problems

Hello,

I was trying to install ACTIONet (R version) on Ubuntu 20.04, but faced a few problems.
Before installing I followed all steps discussed in the tutorial except installing Intel Math Kernel Library (MKL).

Here are my attempts to install ACTIONet in several ways:

R-release version (from Rstudio):
devtools::install_github("shmohammadi86/ACTIONet", ref = "R-release")
This command resulted in the total freezing of the laptop at some point of the installation. I had to force a computer shutdown.
R-devel version (from Rstudio):
devtools::install_github("shmohammadi86/ACTIONet", ref = "R-devel")
The same as for R-release.
R-release version (from terminal):
Installing directly from the clone resulted in the similar issue (computer freezing).
R-devel version (from terminal):
Installing from terminal showed that ACTIONetExperiment package is needed. After installing this package there were a few messages that some files are missing and therefore the installation is impossible.

find: ‘/home/evgenia/SpringProjectGAM/ProjectGAM/year_2/ACTIONet/src/ACTIONet/include’: No such file or directory
find: ‘/home/evgenia/SpringProjectGAM/ProjectGAM/year_2/ACTIONet/src/ACTIONet/include’: No such file or directory
find: ‘/home/evgenia/SpringProjectGAM/ProjectGAM/year_2/ACTIONet/src/ACTIONet/include’: No such file or directory
find: ‘/home/evgenia/SpringProjectGAM/ProjectGAM/year_2/ACTIONet/src/ACTIONet/include’: No such file or directory
In file included from RcppExports.cpp:4:
../inst/include/ACTIONet.h:5:10: fatal error: base.h: No such file or directory
5 | #include <base.h>
| ^~~~~~~~
In file included from RCpp_util.cpp:1:
../inst/include/ACTIONet.h:5:10: fatal error: base.h: No such file or directory
5 | #include <base.h>
| ^~~~~~~~
In file included from ACTIONet.cpp:1:
../inst/include/ACTIONet.h:5:10: fatal error: base.h: No such file or directory
5 | #include <base.h>
| ^~~~~~~~
compilation terminated.
compilation terminated.
compilation terminated.
make: *** [/usr/lib/R/etc/Makeconf:177: RCpp_util.o] Error 1
make: *** Waiting for unfinished jobs....
make: *** [/usr/lib/R/etc/Makeconf:177: ACTIONet.o] Error 1
make: *** [/usr/lib/R/etc/Makeconf:177: RcppExports.o] Error 1
ERROR: compilation failed for package ‘ACTIONet’

removing ‘/home/evgenia/R/x86_64-pc-linux-gnu-library/4.1/ACTIONet’

It would be great if you could help with the installation!
Thank you!

When I attempted to convert Seurat to SingleCellExperiment, I encountered an error.

/what can I do？

@Lioscro

Broken link to download datasets.tar.gz in tutorials

Hi @shmohammadi86,

Could you kindly tell me how to download datasets.tar.gz in tutorials? Thanks so much.

plot.ACTIONet.archetype.footprint error

Hi,

I followed your website's tutorials and keep running into an error when trying the plot.ACTIONet.archetype.fooprint function : "Error in grDevices::rbg(col[1,], col[2,], col[3,], alpha) : alpha level 1.25301, not in [0,1]".

I have run the function's open source code line by line on the data set used in "Interactive visualization, annotation and exploration" tutorial and it appears the problem comes from line 1032 : "scales::alpha(vCol, 0.05 + 0.95 * x/max(x))" as 0.05 + 0.95 * x/max(x) = 1.25301. Using a value between 0 and 1 instead of 0.05 + 0.95 * x/max(x) enables the plot to appear.

Any idea on how to fix this issue with using x in alpha for having a biologically accurate plot ?

Thanks

Error exporting ACE to AnnData

ACE2AnnData function reports the error

Error in apply(catDF, 2, as.character) : 
  dim(X) must have a positive length

Here are the commands that were run.

ace = import.ace.from.10X.h5('pbmc_10k_v3.h5', prefilter = T, min_cells_per_feat = 0.01, min_feats_per_cell = 1000)
ace = reduce.ace(ace, norm_method="none", data_slot="counts")
ace = run.ACTIONet(ace, k_max=5, thread_no=1, data_slot="counts")
ACE2AnnData(ace, main.assay = "counts")

Note that I am using raw counts instead of log counts, and that no normalization is done.

annotate.cells.using.markers issue

I keep getting the following error when I try to use annotate.cells.using.markers() function
Error in compute_marker_aggregate_stats(G = G, S = S, marker_mat = marker_mat, :
internal error: spglue_merge::subview_merge(): count != merge_n_nonzero

Can someone inform me what this means. I can run the test example on the github page with no problems it seems like it could be an issue with my dataset but in some general checks it looks correct.

ace
class: ACTIONetExperiment
dim: 35432 36529
metadata(2): ACTION_sigma backbone
assays(2): counts logcounts
rownames(35432): ENSMMUG00000023296 U6 ... ENSMMUG00000054208
ENSMMUG00000059468
rowData names(0):
colnames(36529): AAACGAAAGCTTGTTG-1_1 AAACGAAAGTCTAGAA-1_1 ...
TTTGTTGGTTCAACGT-1_20 TTTGTTGTCGTGTGAT-1_20
colData names(19): orig.ident nCount_RNA ... assigned_archetype
node_centrality
rowMaps(1): unified_feature_specificity
colMaps(6): ACTION ACTIONred ACTIONet2D ACTIONet3D denovo_color archetype_footprint
rowNets(0):
colNets(1): ACTIONet

Cannot install ACTIONet R

Hello, I have been trying to install this package for days. I first got a cholmod.h error but I resolved it by just copying it into the ACTIONet directory.
However now I am facing other fatal error - pasting the log here:
/Users/samvid_k/ACTIONet/src/ACTIONet/include/clustering/leiden/igraph/vector.pmt:857:47: error: incompatible function pointer types passing 'int (const void *, const void *)' to parameter of type 'int (*)(void *, const void *, const void *)' [-Wincompatible-function-pointer-types] igraph_qsort(vind, n, sizeof(BASE**), FUNCTION(igraph_vector, i_qsort_ind_cmp_desc)); /Users/samvid_k/ACTIONet/src/ACTIONet/include/clustering/leiden/igraph/vector.pmt:859:47: error: incompatible function pointer types passing 'int (const void *, const void *)' to parameter of type 'int (*)(void *, const void *, const void *)' [-Wincompatible-function-pointer-types] igraph_qsort(vind, n, sizeof(BASE**), FUNCTION(igraph_vector, i_qsort_ind_cmp_asc)); In file included from ACTIONet/src/network_tools/leiden/igraph/vector.c:39: /Users/samvid_k/ACTIONet/src/ACTIONet/include/clustering/leiden/igraph/vector.pmt:778:32: error: incompatible function pointer types passing 'int (const void *, const void *)' to parameter of type 'int (*)(void *, const void *, const void *)' [-Wincompatible-function-pointer-types] sizeof(BASE), FUNCTION(igraph_vector, sort_cmp)); /Users/samvid_k/ACTIONet/src/ACTIONet/include/clustering/leiden/igraph/vector.pmt:857:47: error: incompatible function pointer types passing 'int (const void *, const void *)' to parameter of type 'int (*)(void *, const void *, const void *)' [-Wincompatible-function-pointer-types] igraph_qsort(vind, n, sizeof(BASE**), FUNCTION(igraph_vector, i_qsort_ind_cmp_desc)); /Users/samvid_k/ACTIONet/src/ACTIONet/include/clustering/leiden/igraph/vector.pmt:859:47: error: incompatible function pointer types passing 'int (const void *, const void *)' to parameter of type 'int (*)(void *, const void *, const void *)' [-Wincompatible-function-pointer-types] igraph_qsort(vind, n, sizeof(BASE**), FUNCTION(igraph_vector, i_qsort_ind_cmp_asc)); In file included from ACTIONet/src/network_tools/leiden/igraph/vector.c:45: /Users/samvid_k/ACTIONet/src/ACTIONet/include/clustering/leiden/igraph/vector.pmt:778:32: error: incompatible function pointer types passing 'int (const void *, const void *)' to parameter of type 'int (*)(void *, const void *, const void *)' [-Wincompatible-function-pointer-types] sizeof(BASE), FUNCTION(igraph_vector, sort_cmp)); /Users/samvid_k/ACTIONet/src/ACTIONet/include/clustering/leiden/igraph/vector.pmt:857:47: error: incompatible function pointer types passing 'int (const void *, const void *)' to parameter of type 'int (*)(void *, const void *, const void *)' [-Wincompatible-function-pointer-types] igraph_qsort(vind, n, sizeof(BASE**), FUNCTION(igraph_vector, i_qsort_ind_cmp_desc)); /Users/samvid_k/ACTIONet/src/ACTIONet/include/clustering/leiden/igraph/vector.pmt:859:47: error: incompatible function pointer types passing 'int (const void *, const void *)' to parameter of type 'int (*)(void *, const void *, const void *)' [-Wincompatible-function-pointer-types] igraph_qsort(vind, n, sizeof(BASE**), FUNCTION(igraph_vector, i_qsort_ind_cmp_asc)); In file included from ACTIONet/src/network_tools/leiden/igraph/vector.c:51: /Users/samvid_k/ACTIONet/src/ACTIONet/include/clustering/leiden/igraph/vector.pmt:778:32: error: incompatible function pointer types passing 'int (const void *, const void *)' to parameter of type 'int (*)(void *, const void *, const void *)' [-Wincompatible-function-pointer-types] sizeof(BASE), FUNCTION(igraph_vector, sort_cmp)); /Users/samvid_k/ACTIONet/src/ACTIONet/include/clustering/leiden/igraph/vector.pmt:857:47: error: incompatible function pointer types passing 'int (const void *, const void *)' to parameter of type 'int (*)(void *, const void *, const void *)' [-Wincompatible-function-pointer-types] igraph_qsort(vind, n, sizeof(BASE**), FUNCTION(igraph_vector, i_qsort_ind_cmp_desc)); /Users/samvid_k/ACTIONet/src/ACTIONet/include/clustering/leiden/igraph/vector.pmt:859:47: error: incompatible function pointer types passing 'int (const void *, const void *)' to parameter of type 'int (*)(void *, const void *, const void *)' [-Wincompatible-function-pointer-types] igraph_qsort(vind, n, sizeof(BASE**), FUNCTION(igraph_vector, i_qsort_ind_cmp_asc)); In file included from ACTIONet/src/network_tools/leiden/igraph/vector.c:57: /Users/samvid_k/ACTIONet/src/ACTIONet/include/clustering/leiden/igraph/vector.pmt:778:32: error: incompatible function pointer types passing 'int (const void *, const void *)' to parameter of type 'int (*)(void *, const void *, const void *)' [-Wincompatible-function-pointer-types] sizeof(BASE), FUNCTION(igraph_vector, sort_cmp));

Several more similar errors.
Please help me resolve these issues - I really think ACTIONet would help me in my project!

assess.geneset.enrichment.from.archetypes returns 1 fewer genesets than given

I'm finding that the assess.geneset.enrichment.from.archetypes() function returns one fewer gene sets than provided in the membership matrix

ncol(membership_matrix)
> 10

tmp <- assess.geneset.enrichment.from.archetypes(action_list[[1]], associations = membership_matrix)
nrow(tmp$logPvals)
> 9

And it seems that it's always the geneset in the first column of the membership matrix that is lost

colnames(membership_matrix)[2:ncol(membership_matrix)] == rownames(tmp$logPvals)
> TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE

specify additional ACTIONet R deps in README

R CMD INSTALL .

installing to library ‘/opt/anaconda3/envs/sc_tutorial/lib/R/library’
ERROR: dependencies ‘ineq’, ‘rmdformats’, ‘pals’, ‘seriation’, ‘networkD3’, ‘metap’ are not available for package ‘ACTIONet’

Just confirming that these should be added to readme as deps?

Does the Python implementation expect raw counts as input?

It looks like it's normalizing and log-transforming under the hood, but I can't quite follow the C++ code that implements normalize_mat.

Install error (cholmod.h not found; macOS)

Hi there,

Sorry to drop another install error into the issues here. If there is no obvious issue, I can close the issue, but I figured I would include this because it's a fresh macOS installation.

macOS Monterey
MacBook Pro (Apple M1 Max) - fresh OS install

Installed command line tools
homebrew (with /opt/homebrew/bin added to $PATH)
brew install hdf5 suite-sparse
installed gfortran
R 4.1.2 (x86 via Rosetta)
Tried to install actionet

devtools::install_github("shmohammadi86/ACTIONet", ref = "R-release")

Downloading GitHub repo shmohammadi86/ACTIONet@R-release
✓  checking for file ‘/private/var/folders/v3/bfqywp6s08ddpjwj8ynyfmjw0000gn/T/Rtmp1KeRJk/remotes1f397a719e0e/shmohammadi86-ACTIONet-36b7b63/DESCRIPTION’ ...
─  preparing ‘ACTIONet’:
✓  checking DESCRIPTION meta-information ...
─  cleaning src
─  checking for LF line-endings in source and make files and shell scripts
─  checking for empty or unneeded directories
─  looking to see if a ‘data/datalist’ file should be added
─  building ‘ACTIONet_2.1.9.tar.gz’ (1.7s)
   Warning in utils::tar(filepath, pkgname, compression = compression, compression_level = 9L,  :
     storing paths of more than 100 bytes is not portable:
     ‘ACTIONet/inst/include/ACTIONet/nmslib/similarity_search/include/factory/method/pivot_neighb_invindx.h’
   Warning in utils::tar(filepath, pkgname, compression = compression, compression_level = 9L,  :
     storing paths of more than 100 bytes is not portable:
     ‘ACTIONet/inst/include/ACTIONet/nmslib/similarity_search/include/factory/method/simple_inverted_index.h’
   Warning in utils::tar(filepath, pkgname, compression = compression, compression_level = 9L,  :
     storing paths of more than 100 bytes is not portable:
     ‘ACTIONet/inst/include/ACTIONet/nmslib/similarity_search/include/factory/space/space_sparse_dense_fusion.h’
   Warning in utils::tar(filepath, pkgname, compression = compression, compression_level = 9L,  :
     storing paths of more than 100 bytes is not portable:
     ‘ACTIONet/inst/include/ACTIONet/nmslib/similarity_search/include/method/hnsw_distfunc_opt_impl_inline.h’
   
* installing *source* package ‘ACTIONet’ ...
** using staged installation
** libs
Using Mac OS configurations
clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG `find ../inst/include -type d -print | sed s/^/-I/` -w -m64 -DINT_64BITS -DARMA_64BIT_WORD -O2 -march=native -mtune=native -w -m64 -fno-strict-aliasing -fomit-frame-pointer -funroll-loops -fexpensive-optimizations -I/usr/local/opt/suite-sparse/include -DACCELERATE -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/RcppArmadillo/include' -I/usr/local/include  `find ../inst/include -type d -print | sed s/^/-I/` -w -m64 -DINT_64BITS -DARMA_64BIT_WORD -O2 -march=native -mtune=native -w -std=c++14 -m64 -fno-strict-aliasing -fomit-frame-pointer -funroll-loops -fexpensive-optimizations -fPIC  -Wall -g -O2  -c ACTIONet.cpp -o ACTIONet.o

etc

And then the header error

In file included from ACTIONet/misc/my_utils.cc:1:
In file included from ../inst/include/ACTIONet.h:29:
../inst/include/ACTIONet/my_utils.h:5:10: fatal error: 'cholmod.h' file not found
#include "cholmod.h"
         ^~~~~~~~~~~
1 error generated.
make: *** [ACTIONet/misc/my_utils.o] Error 1
make: *** Waiting for unfinished jobs....
In file included from ACTIONet/decomposition/coreset.cc:1:
In file included from ../inst/include/ACTIONet.h:29:
../inst/include/ACTIONet/my_utils.h:5:10: fatal error: 'cholmod.h' file not found
#include "cholmod.h"
         ^~~~~~~~~~~

cholmod.h is in /opt/homebrew/Cellar/suite-sparse/5.10.1_1/include but doesn't seem to be seen.

Do you have any idea what could cause this? Thanks!

AttributeError: module '_ACTIONet' has no attribute 'build_ACTIONet'

Hello,

I tried the following codes:

adata.var_names_make_unique(join='.')
an.pp.filter_adata(adata, min_cells_per_feature=0.01, min_features_per_cell=500) 
sc.pp.normalize_total(adata)
sc.pp.log1p(adata)

an.pp.reduce_kernel(adata)
an.run_ACTIONet(adata)

Everything was fine until I got the error below. How could I fix the error? Thank you.

Running ACTION (22 threads):
Iterating from k = 2 ... 30: 29/29 finished
Joining trace of C & H matrices (depth = 30) ... done (464 archetypes)
Pruning archetypes:
Non-specific archetypes: 3
Unreliable archetypes: 26
Trivial archetypes: 40
Traceback (most recent call last):
File "", line 1, in
File "/root/miniconda3/envs/actionet/lib/python3.8/site-packages/ACTIONet/main.py", line 74, in run_ACTIONet
nt.build_network(
File "/root/miniconda3/envs/actionet/lib/python3.8/site-packages/ACTIONet/network/build.py", line 59, in build_network
G = _an.build_ACTIONet(H_stacked=H_stacked,
AttributeError: module '_ACTIONet' has no attribute 'build_ACTIONet'

Signed_cluster function using run.ACTIONet()

Hi,

I am reanalyzing data using ACTIONet in R, and am running into the following error using run.ACTIONet().

# devtools::install_github("shmohammadi86/ACTIONet", ref = "R-release")
# library(ACTIONet)
# import.sce.from.count.matrix(counts, gene.names)

sce = import.sce.from.Seurat(Menon.seqwell)
sce = reduce.sce(sce) ## Default normalization is 
ACTIONet.out.seqwell = run.ACTIONet(sce)
plot.ACTIONet.interactive(ACTIONet.out.seqwell)

Error in signed_cluster(as(A, "sparseMatrix"), resolution_parameter = resolution) : could not find function "signed_cluster" 2.unify.cell.states(ACTIONet.out, sce, reduction_slot = reduction_slot, sce.data.attr = sce.data.attr, min.cor = unification.min.cor, use.ACTIONet = unification.use.ACTIONet, resolution = unification.resolution) 1.run.ACTIONet(sce)

Until this function everything seems to be working as expected:

Gene set scoring functions don't match vignette

Hi there--fantastic package! Really love its approach.

I'm just going through the vignette and have noticed that the gene set scoring functions may have changed since the vignette. I'm hoping to get geneset enrichment for each archetype along with cell-level scores for each.

Vignette for pathway activity scores:

Pathway.Enrichment = assess.geneset.enrichment(ace = ace, associations = nanoStringDB_human$Immunology)
cell.enrichment.scores = map.cell.scores.from.archetype.enrichment(ace, Pathway.Enrichment)

assess.geneset.enrichment() doesn't seem to exist anymore though. However, I think this has moved to assess.geneset.enrichment.from.archetypes(), which produces a list containing:
$logPvals (is this -log10 or -log?), which has the pathway x archetype p-values, which is great
$thresholds
$scores a genes x archetypes matrix

Does map.cell.scores.from.archetype.enrichment() just want $logPvals, or is it looking for a pathway score x archetype matrix from some function??

plot.ACTIONet error

So now I am trying to run the example from the github page and I can run all of the commands except for this one:

plot.ACTIONet(ace, "celltypes", trans_attr = ace$node_centrality)

Of course, I had to change the option "transparency.attr" to "trans_attr". I get this error:

plot.ACTIONet(ace, "celltypes", trans_attr = ace$node_centrality)
Error in .get_attr_or_split_idx(data, attr = label_attr, return_vec = TRUE) :
Invalid split conditions.

I also get a couple of warnings, one when I run this:
require(ACTIONet)

I get this warning:
Warning message:
replacing previous import 'ggplot2::last_plot' by 'plotly::last_plot' when loading 'ACTIONet'

And when I run this:
ace = import.ace.from.10X.h5('pbmc_10k_v3.h5', prefilter = T, min_cells_per_feat = 0.01, min_feats_per_cell = 1000)

I get this warning:
Warning message:
In Matrix::sparseMatrix(i = indices[] + 1, p = indptr[], x = as.numeric(x = counts.mat[]), :
'giveCsparse' has been deprecated; setting 'repr = "T"' for you

Not sure if those have anything to do with my problem, but I thought I'd include them. Any help would be highly appreciated!

Installation issue

Hello,
I am installing ACTIONNet and have tried all the possible methods listed on the page. However, I am getting this error for every way. Can you please check what is the issue.

**ACTIONet/src/misc/cholmod_wrappers.cc:2:10: fatal error: 'cholmod.h' file not found
#include <cholmod.h>
^~~~~~~~~~~
ACTIONet/src/misc/my_utils.cc:7:10: fatal error: 'cholmod.h' file not found
#include <cholmod.h>
^~~~~~~~~~~
1 error generated.
1 error generated.
make: *** [ACTIONet/src/misc/cholmod_wrappers.o] Error 1
make: *** Waiting for unfinished jobs....
make: *** [ACTIONet/src/misc/my_utils.o] Error 1
ACTIONet/src/network_tools/network_diffusion.cc:6:10: fatal error: 'cholmod.h' file not found
#include <cholmod.h>
^~~~~~~~~~~
1 error generated.
make: *** [ACTIONet/src/network_tools/network_diffusion.o] Error 1
ERROR: compilation failed for package ‘ACTIONet’

removing ‘/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/ACTIONet’**

Will be very grateful!

Installing error Windows 10

Hello,

I'm trying to install ACTIONet (R version) on Windows 10 using the command devtools::install_github("shmohammadi86/ACTIONet", ref = "R-release" but I get the following error :

Makevars:40: *** Unsupported OS MSYS_NT-10.0-19042. Stop.

Is Windows 10 supported by your package ? If so, is there a way to solve this issue ?

Thank you for your help !

Install Error: ACTIONet/src/decomposition/ACTION.cc:2:10: fatal error: cholmod.h: No such file or directory

Docker

Hello,

I was trying to use docker for running ACTIONet, but it appeared that no packages for single-cell analysis are installed (ACTIONet as well).

I was running docker as described in the tutorial:
docker run -p 8787:8787 shmohammadi86/actionet

terminal output:

[s6-init] making user provided files available at /var/run/s6/etc...exited 0.
[s6-init] ensuring user provided files have correct perms...exited 0.
[fix-attrs.d] applying ownership & permissions fixes...
[fix-attrs.d] done.
[cont-init.d] executing container initialization scripts...
[cont-init.d] userconf: executing... 
tput: No value for $TERM and no -T specified
tput: No value for $TERM and no -T specified


tput: No value for $TERM and no -T specified
ERROR: You must set a unique PASSWORD (not 'rstudio') first! e.g. run with:
docker run -e PASSWORD=<YOUR_PASS> -p 8787:8787 rocker/rstudio
tput: No value for $TERM and no -T specified


[cont-init.d] userconf: exited 1.
[cont-init.d] done.
[services.d] starting services
[services.d] done.

Running with setting the password (as it was said in the error) doesn't fix the problem.

Running Rstudio Server on http://127.0.0.1:8787 and here is the output from Rstudio console:

During startup - Warning messages:
1: In library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE, :
there is no package called ‘BiocManager’
2: package ‘BiocManager’ in options("defaultPackages") was not found

library(ACTIONet)
Error in library(ACTIONet) : there is no package called ‘ACTIONet’

sessionInfo()
R version 4.0.3 (2020-10-10)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 20.04.1 LTS

Matrix products: default
BLAS: /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.9.0
LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.9.0

locale:
[1] LC_CTYPE=C.UTF-8 LC_NUMERIC=C LC_TIME=C.UTF-8 LC_COLLATE=C.UTF-8
[5] LC_MONETARY=C.UTF-8 LC_MESSAGES=C LC_PAPER=C.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C LC_MEASUREMENT=C.UTF-8 LC_IDENTIFICATION=C

attached base packages:
[1] stats graphics grDevices utils datasets methods base

loaded via a namespace (and not attached):
[1] compiler_4.0.3 tools_4.0.3

What can be the problem here? and how it should be fixed?

Thanks!

How to obtain an adjacency matrix for cluster.graph

Hi,

I was trying to use a wrapper function for the leiden algorithm, cluster.graph. It is not clear to me how to obtain an input adjacency matrix from a SCE/ACE object. I am currently using v3.0.2.

For older versions, Leiden.clustering seems to be used for the leiden clustering. The input was an SCE/ACE object instead of an adjacency matrix.

Best,
Joon

Problem Installing

Hello,

I am trying to install ACTIONet in Python. I followed the directions. I installed brew and then proceeded with pip install. When I go to pip installation, it can't find the compatible version of all the different packages. Therefore the installation freezes.

Is there a way to fix this? Could you tell me which version of hdf5 etcetera you had installed.

Error running SingleCellExperiment data

Hi,

I pull the docker and was running

ace <- SingleCellExperiment(assays=list(logcounts=log2(data+0.1^10)))
ace = reduce.ace(ace)

and got this error

Error in reduce_kernel(S = S, reduced_dim = reduced_dim, iter = max_iter, :
Not an S4 object.

Can you guide me to get it running properly?
Thanks.

AttributeError: module 'ACTIONet' has no attribute 'pp'

Hi,
I was running the python version and got the following error:

AttributeError: module 'ACTIONet' has no attribute 'pp'

Could you please guide me to the solution?
Thanks.

Feature: Provide archetypes for SCINET

Hi,

Is it possible to provide the amount of the specific cell types beforehand to ACTION or SCINET? For example, say I have downloaded a public scRNA object which already has all the celltypes assigned, e.g. 15 different cell types. Is it possible to specify the number of archetypes, 15 in this case, that ACTION should compute?

Is it possible to provide the celltypes to SCINET and say: I want you to construct a scRNA-network specifically for these celltypes (all annotations are available).

Thanks already for all your help!

Error drawing with ACE2AnnData and plot.ACTIONet(ace) command

Hi,

I am trying to run the “Example Run” using ‘pbmc_10k_v3.h5’ based on your website’s tutorials. I have seen errors when I was drawing "plot.ACTIONet(ace, "celltypes", transparency.attr = ace$node_centrality)" and following "ACE2AnnData" to export the results.

Do you have any idea to solve the issues?

Am I something wrong or missing packages which need to be installed?

Thank you.

ace = import.ace.from.10X.h5('pbmc_10k_v3.h5', prefilter = T, min_cells_per_feat = 0.01, min_feats_per_cell = 1000)
ace = normalize.ace(ace)
ace = reduce.ace(ace)

Computing reduced ACTION kernel (sparse):
Performing SVD on original matrix: IRLB_ (sparse) -- A: 12075 x 10744
Computing perturbed SVD ... done

ace = run.ACTIONet(ace)
Running ACTION (14 threads):
Iterating from k = 2 ... 40: 39/39 finished
Joining trace of C & H matrices (depth = 40) ... done (819 archetypes)
Pruning archetypes:
Non-specific archetypes: 12
Unreliable archetypes: 72
Trivial archetypes: 73
Building adaptive network (14 threads):
Parameters: density = 1.00, mutual_edges_only = TRUE
Building index ... done
Constructing k*-NN ... done
Finalizing network ... done
Computing layout (14 threads):
Parameters: layout_epochs = 1000
Computing 2D layout ... done
Computing 3D layout ... done
Computing node colors ... done
Unifying 667 archetypes (14 threads):
Parameters: alpha = 0.99, sensitivity = 0.00
Running network diffusion
26 unified states (sensitivity = 0.70)
Computing feature specificity ... done

data("curatedMarkers_human")
markers = curatedMarkers_human$Blood$PBMC$Ding2019$marker.genes
annot.out = annotate.cells.using.markers(ace, markers)
ace$celltypes = annot.out$Labels
plot.ACTIONet(ace, "celltypes", transparency.attr = ace$node_centrality)

Error in plot.ACTIONet(ace, "celltypes", transparency.attr = ace$node_centrality) :
unused argument (transparency.attr = ace$node_centrality)

ACE2AnnData(ace, fname = "pbmc_10k_v3.h5ad")

Error in ACE2AnnData(ace, fname = "pbmc_10k_v3.h5ad") :
unused argument (fname = "pbmc_10k_v3.h5ad")

plot.ACTIONet(ace)
ACE2AnnData(ace, fname = "pbmc_10k_v3.h5ad")

Error in ACE2AnnData(ace, fname = "pbmc_10k_v3.h5ad") :
unused argument (fname = "pbmc_10k_v3.h5ad")

shmohammadi86 / actionet Goto Github PK

actionet's Introduction

ACTIONet R Package

ACTIONet Python Package

How to get more help and file bug reports

actionet's People

Contributors

Stargazers

Watchers

Forkers

actionet's Issues

Recommend Projects

Recommend Topics

Recommend Org