xlucpu / movics Goto Github PK
View Code? Open in Web Editor NEWMulti-Omics integration and VIsualization in Cancer Subtyping
License: Other
Multi-Omics integration and VIsualization in Cancer Subtyping
License: Other
Hi Xiao-fan,
Thanks for your package, however, I still have some errors in installation.
ld: warning: directory not found for option '-L/usr/local/gfortran/lib/gcc/x86_64-apple-darwin18/8.2.0'
ld: warning: directory not found for option '-L/usr/local/gfortran/lib'
ld: library not found for -lgfortran
clang: error: linker command failed with exit code 1 (use -v to see invocation)
make: *** [CIMLR.so] Error 1
ERROR: compilation failed for package ‘CIMLR’
* removing ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library/CIMLR’
Error: Failed to install 'MOVICS' from GitHub:
Failed to install 'CIMLR' from GitHub:
(converted from warning) installation of package ‘/var/folders/h1/wph5l7kn6sq020007z1bq2d00000gn/T//RtmpQHMklX/filef791774317eb/CIMLR_1.0.0.tar.gz’ had non-zero exit status
>
Dr. XF:
I found that I cannot install MOVICS in my RStudio workstation. I tried many times, but I faced the same error is :
object 'geom_table' is not exported by 'namespace:ggpmisc'
How to solve this problems? please , thank you !
> cmoic.brca <- getConsensusMOIC(moic.res.list = moic.res.list,
+ fig.name = "CONSENSUS HEATMAP",
+ distance = "euclidean",
+ linkage = "average")
Error: C stack usage 7969424 is too close to the limit
Graphics error: Plot rendering error
Error: C stack usage 7969280 is too close to the limit
Graphics error: Plot rendering error
Error: C stack usage 7969328 is too close to the limit
Graphics error: Plot rendering error
Error: C stack usage 7969360 is too close to the limit
Graphics error: Plot rendering error
Error: C stack usage 7969232 is too close to the limit
Graphics error: Plot rendering error
Error: C stack usage 7969376 is too close to the limit
Graphics error: Plot rendering error
Error: C stack usage 7969248 is too close to the limit
Graphics error: Plot rendering error
Error: C stack usage 7969232 is too close to the limit
Graphics error: Plot rendering error
Error: C stack usage 7969312 is too close to the limit
Graphics error: Plot rendering error
Error: C stack usage 7969408 is too close to the limit
Graphics error: Plot rendering error
Error: C stack usage 7969408 is too close to the limit
Graphics error: Plot rendering error
Error: C stack usage 7969184 is too close to the limit
Graphics error: Plot rendering error
Error: C stack usage 7969184 is too close to the limit
Graphics error: Plot rendering error
Error: C stack usage 7969200 is too close to the limit
Graphics error: Plot rendering error
Error: C stack usage 7969200 is too close to the limit
Graphics error: Plot rendering error
Error: C stack usage 7969280 is too close to the limit
Graphics error: Plot rendering error
Error: C stack usage 7969296 is too close to the limit
Graphics error: Plot rendering error
my PC information
sessionInfo()
R version 4.0.2 (2020-06-22)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: CentOS Linux 7 (Core)
Matrix products: default
BLAS: /usr/local/lib64/R/lib/libRblas.so
LAPACK: /usr/local/lib64/R/lib/libRlapack.so
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=en_US.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] parallel stats graphics grDevices utils datasets methods
[8] base
other attached packages:
[1] dplyr_1.0.2 MOVICS_0.99.5 Biobase_2.50.0
[4] BiocGenerics_0.36.0 kableExtra_1.3.1 knitr_1.30
loaded via a namespace (and not attached):
[1] rappdirs_0.3.1 CIMLR_1.0.0
[3] tableone_0.12.0 oompaData_3.1.1
[5] InterSIM_2.2.0 ggpmisc_0.3.6
[7] pkgmaker_0.32.2 tidyr_1.1.2
[9] ggplot2_3.3.2 bit64_4.0.5
[11] irlba_2.3.3 DelayedArray_0.16.0
[13] data.table_1.13.2 RCurl_1.98-1.2
[15] doParallel_1.0.16 generics_0.1.0
[17] preprocessCore_1.52.0 cowplot_1.1.0
[19] RSQLite_2.2.1 shadowtext_0.0.7
[21] bit_4.0.4 enrichplot_1.10.0
[23] webshot_0.5.2 xml2_1.3.2
[25] SummarizedExperiment_1.20.0 assertthat_0.2.1
[27] viridis_0.5.1 xfun_0.19
[29] hms_0.5.3 evaluate_0.14
[31] caTools_1.18.0 readxl_1.3.1
[33] km.ci_0.5-2 igraph_1.2.6
[35] DBI_1.1.0 geneplotter_1.68.0
[37] stats4_4.0.2 purrr_0.3.4
[39] ellipsis_0.3.1 iClusterPlus_1.26.0
[41] ggpubr_0.4.0 backports_1.2.0
[43] permute_0.9-5 survey_4.0
[45] geepack_1.3-1 annotate_1.68.0
[47] gridBase_0.4-7 RcppParallel_5.0.2
[49] MatrixGenerics_1.2.0 vctrs_0.3.4
[51] ggalluvial_0.12.2 Cairo_1.5-12.2
[53] maftools_2.6.0 jstable_1.0.0
[55] entropy_1.2.1 abind_1.4-5
[57] withr_2.3.0 ggforce_0.3.2
[59] bdsmatrix_1.3-4 checkmate_2.0.0
[61] vegan_2.5-6 mclust_5.4.6
[63] cluster_2.1.0 DOSE_3.16.0
[65] alluvial_0.1-2 CMScaller_0.99.2
[67] crayon_1.3.4 genefilter_1.72.0
[69] edgeR_3.32.0 pkgconfig_2.0.3
[71] tweenr_1.0.1 GenomeInfoDb_1.26.0
[73] nlme_3.1-148 rlang_0.4.8
[75] lifecycle_0.2.0 downloader_0.4
[77] registry_0.5-1 cellranger_1.1.0
[79] polyclip_1.10-0 GSVA_1.38.0
[81] matrixStats_0.57.0 PINSPlus_2.0.5
[83] pamr_1.56.1 graph_1.68.0
[85] rngtools_1.5 Matrix_1.2-18
[87] KMsurv_0.1-5 carData_3.0-4
[89] heatmap.plus_1.3 boot_1.3-25
[91] zoo_1.8-8 GlobalOptions_0.1.2
[93] png_0.1-7 viridisLite_0.3.0
[95] rjson_0.2.20 oompaBase_3.2.9
[97] bitops_1.0-6 ConsensusClusterPlus_1.54.0
[99] KernSmooth_2.23-17 blob_1.2.1
[101] shape_1.4.5 stringr_1.4.0
[103] qvalue_2.22.0 rstatix_0.6.0
[105] S4Vectors_0.28.0 ggsignif_0.6.0
[107] scales_1.1.1 memoise_1.1.0
[109] graphite_1.36.0 GSEABase_1.52.0
[111] magrittr_1.5 plyr_1.8.6
[113] gplots_3.1.0 zlibbioc_1.36.0
[115] compiler_4.0.2 scatterpie_0.1.5
[117] mogsa_1.24.0 RColorBrewer_1.1-2
[119] lme4_1.1-25 clue_0.3-57
[121] DESeq2_1.30.0 XVector_0.30.0
[123] patchwork_1.0.1 MASS_7.3-51.6
[125] mgcv_1.8-31 tidyselect_1.1.0
[127] stringi_1.5.3 forcats_0.5.0
[129] prettyGraphs_2.1.6 mitools_2.4
[131] GOSemSim_2.16.1 locfit_1.5-9.4
[133] ggrepel_0.8.2 survMisc_0.5.5
[135] grid_4.0.2 fastmatch_1.1-0
[137] tools_4.0.2 rio_0.5.16
[139] uuid_0.1-4 circlize_0.4.11
[141] rstudioapi_0.11 foreach_1.5.1
[143] foreign_0.8-80 clusterRepro_0.9
[145] coxme_2.2-16 gridExtra_2.3
[147] farver_2.0.3 ggraph_2.0.3
[149] digest_0.6.27 rvcheck_0.1.8
[151] BiocManager_1.30.10 flexclust_1.4-0
[153] FNN_1.1.3 Rcpp_1.0.5
[155] GenomicRanges_1.42.0 car_3.0-10
[157] ClassDiscovery_3.3.12 broom_0.7.2
[159] httr_1.4.2 survminer_0.4.8
[161] AnnotationDbi_1.52.0 ComplexHeatmap_2.7.1
[163] colorspace_1.4-1 rvest_0.3.6
[165] XML_3.99-0.5 IRanges_2.24.0
[167] splines_4.0.2 statmod_1.4.35
[169] graphlayouts_0.7.1 xtable_1.8-4
[171] nloptr_1.2.2.2 SNFtool_2.3.0
[173] tidygraph_1.2.0 corpcor_1.6.9
[175] modeltools_0.2-23 ExPosition_2.8.23
[177] R6_2.5.0 ridge_2.7
[179] pillar_1.4.6 htmltools_0.5.0
[181] NMF_0.23.0 minqa_1.2.4
[183] glue_1.4.2 clusterProfiler_3.18.0
[185] BiocParallel_1.24.1 class_7.3-17
[187] codetools_0.2-16 aricode_1.0.0
[189] fgsea_1.16.0 lattice_0.20-41
[191] tibble_3.0.4 sva_3.38.0
[193] curl_4.3 svd_0.5
[195] officer_0.3.15 gtools_3.8.2
[197] IntNMF_1.2.0 zip_2.1.1
[199] GO.db_3.12.1 openxlsx_4.2.3
[201] coca_1.1.0 survival_3.1-12
[203] limma_3.46.0 rmarkdown_2.5
[205] munsell_0.5.0 DO.db_2.9
[207] GetoptLong_1.0.4 GenomeInfoDbData_1.2.4
[209] iterators_1.0.13 labelled_2.7.0
[211] impute_1.64.0 haven_2.3.1
[213] reshape2_1.4.4 gtable_0.3.0
However,
according to those links:
https://sr-c.github.io/2019/02/16/Error-C-stack-usage-is-too-close-to-the-limit/
LifeWorks/biojazz#9
(base) [zhou@localhost strelka2]$ ulimit -s 16384
(base) [zhou@localhost strelka2]$ R --slave -e 'Cstack_info()["size"]'
size
15938355
(base) [zhou@localhost strelka2]$ ulimit -s 102400
bash: ulimit: stack size: cannot modify limit: Operation not permitted
(base) [zhou@localhost strelka2]$ ulimit -s 102400
bash: ulimit: stack size: cannot modify limit: Operation not permitted
(base) [zhou@localhost strelka2]$ ulimit -m unlimited
(base) [zhou@localhost strelka2]$ ulimit -s unlimited
bash: ulimit: stack size: cannot modify limit: Operation not permitted
(base) [zhou@localhost strelka2]$ conda activate strelka2
R function "getConsensusMOIC" gets consensus from different algorithms, so I have a question about how to select the best combination. I know the silhouette is the evaluation indicator. But in my test, the combination having 0.9 silhouette does not have a survival difference. So if I wanna compare the difference and select the best, which functions I can perform, or whether you have a try.
Hi Dr. Xiaofan,
MOVICS is fantastic. When installing this package, I am curious about how to install on R 3.6.0. Would you please offer some help?
Best,
Yingcheng
yau.pam.pred <- runPAM(train.expr = fpkm,
moic.res = cmoic.brca,
test.expr = brca.yau$mRNA.expr)
--all samples matched.
--a total of 8545 genes shared and used.
--log2 transformation done for training expression data.
--testing expression profile seems to have been standardised (z-score or log transformation), no more action will be performed.
Error in quantile.default(sd, offset.percent/100) :
'na.rm'如果设为FALSE的话不允许有遺漏值和NaN
I'm sure there's no NA.
Hi, I'm getting new errors when trying to install the package:
* installing *source* package ‘MOVICS’ ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
Error: object ‘get_fun_from_pkg’ is not exported by 'namespace:rvcheck'
Execution halted
ERROR: lazy loading failed for package ‘MOVICS’
* removing ‘/home/prvst/R/x86_64-pc-linux-gnu-library/4.0/MOVICS’
Warning message:
In i.p(...) :
installation of package ‘/tmp/RtmpKdm5a1/file284e6df30d7/MOVICS_0.99.17.tar.gz’ had non-zero exit status
I'm on a Linux system, using R 4.0.4
Hi, I tried to install MOVICS but could not do it because one of the dependencies is now deprecated and not available for R's latest version.
Error: Failed to install 'MOVICS' from GitHub: (converted from warning) package ‘SNFtool’ is not available for this version of R
The package SNFtool was removed from CRAN.
Hi,
I ran a problem with my copy number data in a position by sample matrix. Binary data of mutations are ok.
#Part of my copy number
[TAB] BRA08.T BRA10.T BRA13.T BRA15.T KAL0004.T
1_108276812_108276812 -0.000720281 -0.454077 0.0047503 0.00339646 0.255127
1_108276813_108286811 -0.000720281 -0.454077 0.0047503 0.00339646 0.255127
1_108286812_108286812 -0.000720281 -0.454077 0.0047503 0.00339646 0.255127
1_108286813_108296810 -0.000720281 -0.454077 0.0047503 0.00339646 0.255127
1_108296811_108296811 -0.000720281 -0.454077 0.0047503 0.00339646 0.255127
1_108296812_108306810 -0.000720281 -0.454077 0.0047503 0.00339646 0.255127
[TAB] KAL0013.T KAL0022.T KAL0043.T KAL0054.T KAL0072.T
1_108276812_108276812 -0.425851 0.0213336 -0.200039 0.00249974 -0.103276
1_108276813_108286811 -0.425851 0.0213336 -0.200039 0.00249974 -0.103276
1_108286812_108286812 -0.425851 0.0213336 -0.200039 0.00249974 -0.103276
1_108286813_108296810 -0.425851 0.0213336 -0.200039 0.00249974 -0.103276
1_108296811_108296811 -0.425851 0.0213336 -0.200039 0.00249974 -0.103276
1_108296812_108306810 -0.425851 0.0213336 -0.200039 0.00249974 -0.103276
#Command
Hrpcaall <- list(omics1 = Hrpcassm_mat,
omics2 = Hrpcacna_data )
optk.hrpca <- getClustNum(data = Hrpcaall,
is.binary = c(T,F),
try.N.clust = 2:6,
fig.name = "CLUSTER NUMBER")
90% complete
95% complete
100% complete
calculating Gap-statistics...
Error in svd(B, nv = 0) : infinite or missing values in 'x'
Calls: getClustNum ... -> msvd -> svd.sol -> nsmall.svd -> svd
Execution halted
I tried to transform data by adding +20 or round numbers to 3 digits. It still didn't work. I am not sure what causes the error. It seems not to be negative numbers. Or is it about column names? Your suggestion would be appreciated. I tried to debug myself for many days.
Thanks,
James
Thanks for such a wonderful package.
is there a conda version
and can it be installed in R3.6.3. I see your manual docs saying it needs R4.0.1
The windows exhibited:
Warning in .recacheSubclasses(def@className, def, env) :
undefined subclass "numericVector" of class "Mnumeric"; definition not updated
错误: 'namespace:ggpmisc'没有出口'geom_table'这个对象
停止执行
The same error occurred after a successful installation.
Hi,
Thanks for your perfect package. I have problem in in compTMB() command. I have prepared my input data according to your sample file and instructions. But, it shows error:
#######################
--89 samples mismatched from current subtypes.
-Validating
--Removed 4190 duplicated variants
-Silent variants: 70969
-Summarizing
--Possible FLAGS among top ten genes:
TTN
SYNE1
MUC16
OBSCN
-Processing clinical data
--Missing clinical data
-Finished in 2.840s elapsed (2.660s cpu)
Error in .rowNamesDF<-
(x, value = value) :
duplicate 'row.names' are not allowed
In addition: Warning message:
non-unique values when setting 'row.names':
##############################
Then I deleted entire rows with "-" values in nucleotide columns (the last three columns). Then it shows this error:
#############################
--89 samples mismatched from current subtypes.
-Validating
--Removed 3712 duplicated variants
-Silent variants: 65787
-Summarizing
--Possible FLAGS among top ten genes:
TTN
MUC16
SYNE1
OBSCN
-Processing clinical data
--Missing clinical data
-Finished in 2.840s elapsed (2.610s cpu)
Error in .rowNamesDF<-
(x, value = value) :
missing values in 'row.names' are not allowed
##############################
Then I deleted all nucleotide which were non SNP and finally it works. But, unfortunately the results was not reasonable (not significant that I know it should be significant among 4 clusters).
I will be thankful if you help me in this regard.
HI
When I install MOVICS (devtools::install_github("xlucpu/MOVICS")), I get this problem Error: objects ‘rowSums’, ‘colSums’, ‘rowMeans’, ‘colMeans’ are not exported by 'namespace:BiocGenerics'
Execution halted
My biocgenerics version is 0.47.0
sessionInfo()
`R version 4.3.0 (2023-04-21)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 20.04.5 LTS
Matrix products: default
BLAS/LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/libopenblasp-r0.3.8.so; LAPACK version 3.9.0
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=en_US.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
time zone: Asia/Shanghai
tzcode source: system (glibc)
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] BiocGenerics_0.47.0
loaded via a namespace (and not attached):
[1] miniUI_0.1.1.1 compiler_4.3.0 BiocManager_1.30.22
[4] crayon_1.5.2 promises_1.2.0.1 Rcpp_1.0.10
[7] stringr_1.5.0 callr_3.7.3 later_1.3.1
[10] fastmap_1.1.1 mime_0.12 R6_2.5.1
[13] curl_5.0.0 htmlwidgets_1.6.2 desc_1.4.2
[16] profvis_0.3.8 rprojroot_2.0.3 shiny_1.7.4
[19] rlang_1.1.1 cachem_1.0.8 stringi_1.7.12
[22] httpuv_1.6.11 fs_1.6.2 pkgload_1.3.2
[25] memoise_2.0.1 cli_3.6.1 withr_2.5.0
[28] magrittr_2.0.3 ps_1.7.5 digest_0.6.31
[31] processx_3.8.1 rstudioapi_0.14 xtable_1.8-4
[34] remotes_2.4.2 devtools_2.4.5 lifecycle_1.0.3
[37] prettyunits_1.1.1 vctrs_0.6.2 glue_1.6.2
[40] urlchecker_1.0.1 sessioninfo_1.2.2 pkgbuild_1.4.0
[43] purrr_1.0.1 usethis_2.1.6 tools_4.3.0
[46] ellipsis_0.3.2 htmltools_0.5.5 `
Hope you could help me fix it.
install.packages("~/R/x86_64-pc-linux-gnu-library/MOVICS-master.tar.gz", repos = NULL, type = "source")
将程序包安装入‘/home/guozhuangjie/R/x86_64-pc-linux-gnu-library/4.3’
(因为‘lib’没有被指定)
ERROR: dependency ‘CIMLR’ is not available for package ‘MOVICS’
install.packages("/home/guozhuangjie/R/x86_64-pc-linux-gnu-library/CIMLR-1.0.0_R.tar.gz", repos = NULL, type = "source")
将程序包安装入‘/home/guozhuangjie/R/x86_64-pc-linux-gnu-library/4.3’
(因为‘lib’没有被指定)
that is all .who can help me plz. thank you
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.