omarwagih / rweblogo Goto Github PK

alg <- c('CCAACCCAA', 'CCAACCCTA', 'AAAGCCTGA', 'TGAACCGGA')
weblogo(alg)

creates and empty file but gives no warnings.

It would be great to have support for MultipleAlignment objects from Biostrings. In theory one could also extract the sequences as a vector from a MultipleAlignment object and use those for weblogo, but I don't know how to do this.

I get an error even with the example input:

aln <- c('CCAACCCAA', 'CCAACCCTA', 'AAAGCCTGA', 'TGAACCGGA')
weblogo(seqs=aln, return.cmd = TRUE)

Error: The truth value of an array with more than one element is ambiguous. Use a.any() or a.all()
Sequence logo saved to /home/kalimero/Desktop/SINEs/RWebLogo.pdf
[1] "/home/kalimero/R/x86_64-pc-linux-gnu-library/3.6/RWebLogo/extdata/weblogo-3.3/weblogo < /tmp/RtmpkgFUnN/tmp.logo > /home/kalimero/Desktop/SINEs/RWebLogo.pdf --format 'pdf' --size 'large' --fineprint ''"

sessionInfo()

R version 3.6.1 (2019-07-05)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 18.04.3 LTS

Matrix products: default
BLAS: /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.7.1
LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.7.1

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

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

other attached packages:
[1] RWebLogo_1.0.3

loaded via a namespace (and not attached):
[1] compiler_3.6.1 tools_3.6.1 findpython_1.0.5

python --version

Python 2.7.15+

python3 --version

Python 3.6.8

How can I solve this?

Thank you.

Hi Omar Wagih,

I have a problem with the RWebLogo package.
I have nice Alignment of Short Peptide stretches.
Everything works fine, but when I create the plots, some lines appear.
Any idea what I'm doing wrong?

Line I use to call the weblogo function:
weblogo(open=FALSE,seqs=test6$Sequence,size="large",scale.width = FALSE,aspect.ratio = 2.2,file.out= paste("./Plots/Weblogos/",chotnumsnames[j],"Weblogo",subgroup,".pdf",sep=""),sequence.type="protein",composition="none",units="probability",annotate=Chothianums,errorbars=FALSE,color.scheme="chemistry")

Pdf I get:
L95Chothia_Weblogo_Kiii.pdf

As you see there are some annoying lines in the final product. Did I miss a variable? Or use some wrong setting?

Cheers,
Rob

Python is in my path by weblogo fails to find it.

weblogo(file.in='trb.phy')
Traceback (most recent call last):
File "/home/chad/R/x86_64-conda_cos6-linux-gnu-library/3.5/RWebLogo/extdata/weblogo-3.3/weblogo", line 56, in
import weblogolib._cli
File "/home/chad/R/x86_64-conda_cos6-linux-gnu-library/3.5/RWebLogo/extdata/weblogo-3.3/weblogolib/init.py", line 104
print "You need python 2 or 3!"
^
SyntaxError: Missing parentheses in call to 'print'. Did you mean print("You need python 2 or 3!")?
Sequence logo saved to /home/chad/mixcr/RWebLogo.pdf
history()
py_config()
python: /home/chad/miniconda3/bin/python
libpython: /home/chad/miniconda3/lib/libpython3.7m.so
pythonhome: /home/chad/miniconda3:/home/chad/miniconda3
version: 3.7.3 (default, Mar 27 2019, 22:11:17) [GCC 7.3.0]
numpy: /home/chad/miniconda3/lib/python3.7/site-packages/numpy
numpy_version: 1.16.3

python versions found:
/home/chad/miniconda3/bin/python
/usr/bin/python
/usr/bin/python3

sessionInfo()
R version 3.5.1 (2018-07-02)
Platform: x86_64-conda_cos6-linux-gnu (64-bit)
Running under: Ubuntu 19.04

Matrix products: default
BLAS/LAPACK: /usr/local/share/bcbio/anaconda/lib/R/lib/libRblas.so

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

attached base packages:
[1] stats4 parallel datasets utils grDevices graphics stats methods base

other attached packages:
[1] reticulate_1.12 RWebLogo_1.0.3 muscle_3.24.0 Biostrings_2.50.2 XVector_0.22.0 IRanges_2.16.0 S4Vectors_0.20.1 BiocGenerics_0.28.0 rmarkdown_1.12
[10] knitr_1.22 vegan_2.5-5 permute_0.9-5 gridExtra_2.3 MASS_7.3-51.4 plyr_1.8.4 colorspace_1.4-1 car_3.0-2 carData_3.0-2
[19] reshape2_1.4.3 gdata_2.18.0 ggplot2_3.1.1 lattice_0.20-38

loaded via a namespace (and not attached):
[1] Rcpp_1.0.1 gtools_3.8.1 assertthat_0.2.1 digest_0.6.18 R6_2.4.0 cellranger_1.1.0 evaluate_0.13 highr_0.8 pillar_1.3.1 zlibbioc_1.28.0
[11] rlang_0.3.4 lazyeval_0.2.2 curl_3.3 readxl_1.3.1 data.table_1.12.2 Matrix_1.2-17 labeling_0.3 splines_3.5.1 stringr_1.4.0 foreign_0.8-71
[21] munsell_0.5.0 compiler_3.5.1 xfun_0.6 pkgconfig_2.0.2 findpython_1.0.5 mgcv_1.8-28 htmltools_0.3.6 tcltk_3.5.1 tidyselect_0.2.5 tibble_2.1.1
[31] rio_0.5.16 crayon_1.3.4 dplyr_0.8.0.1 withr_2.1.2 grid_3.5.1 jsonlite_1.6 nlme_3.1-139 gtable_0.3.0 magrittr_1.5 scales_1.0.0
[41] zip_2.0.1 stringi_1.4.3 openxlsx_4.1.0 RColorBrewer_1.1-2 tools_3.5.1 forcats_0.4.0 glue_1.3.1 purrr_0.3.2 hms_0.4.2 abind_1.4-5
[51] yaml_2.2.0 cluster_2.0.9 BiocManager_1.30.4 haven_2.1.0