ts404 / alignstat Goto Github PK

Rename to match_summary and add a number giving global average match score

Check that degapped sequences in both alignments are identical

Use more understandable names for $means and $results in align_alignments output.

$means --> $identity
$results --> $classification

Will need to update plot arguments and readme to reflect changes

Add item $score with global mean score
Fix examples for plots so they work with this structure

Generate a heatmap that simply uses colour to indicate Match / Merge / Split / Shift / Gapcon for each position in the reference alignment.

moved PAC$results[10,1](the score) to be its own item in the PAC list i.e. PAC$score

However, this now means that naming the rows creates an error since the row number is wrong. Probably needs fix in the rcpp

To:

plot_alignment_heatmap
plot_match_summary
plot_category_proportions

So that the naming is a little more consistent

Hello
I am interested in using alignstat to compare various alignment algorithm
I tried the online version but it does not seem to work: fasta alignments are loaded but nothing happen afterward.
I also installed the r package but I get an error message....
I tried loading my alignment with phylotools::read.fasta or with ape but I still have this error:
Error in path.expand(file) : invalid 'path' argument
In addition: Warning messages:
1: In if (tools::file_ext(alignment) == "clustal" | tools::file_ext(alignment) == :
the condition has length > 1 and only the first element will be used
2: In if (tools::file_ext(alignment) == "msf" | tools::file_ext(alignment) == :
the condition has length > 1 and only the first element will be used
3: In if (tools::file_ext(alignment) == "mase" | tools::file_ext(alignment) == :
the condition has length > 1 and only the first element will be used

I tried with alignments in msa or fasta format...
class(myFirstAlignment)
[1] "MsaAAMultipleAlignment"
attr(,"package")
[1] "msa"

or with
ref_df=phylotools::read.fasta(ref)
class(ref_df)
[1] "data.frame"

any suggestions?

For Plots.R and compare_alignments.R

• Emit sensible error if alignments are of different lengths
• Consider adding functionality estimate sum-of-pairs true positive (SPFP) and sum-of-pairs false negative (SPFN) scores of the estimated alignment on a per column basis
• Consider ordering based on common names between MSAs rather than requiring MSAs to be in a fixed order

Do this plot with ggplot geom_tile

http://www.inside-r.org/packages/cran/seqinr/docs/read.alignment

When first installing:

library("AlikeAlignmentAligner", lib.loc="~/R/win-library/3.1")

Attaching package: ‘AlikeAlignmentAligner’
The following object is masked by ‘.GlobalEnv’:
percent

Warning message:
"package 'AlignStat' is not available for this version of R
A version of this package for your version of R might be available elsewhere,
see the ideas at https://cran.r-project.org/doc/manuals/r-patched/R-admin.html#Installing-packages"

Place match_summary_plot "Av= xx.x%" score over with the legend?

edit plots so that they simply require the res_list as an argument input, rather than specific list items (res_list$xxx). No other inputs really make sense other than the specific output file of align_alignments.

Hello!

After modifying my alignments as best as possible to match the data.frame format of the example dataset ("reference_alignment"), I am receiving an error stating that the alignments do not contain the same set of sequences, even though they do. Below is the code I used to covert the alignments to data frames, and I have attached the fasta files (/Data) I would like to compare. Any help would be appreciated!
Data.zip

## R script ######
library("AlignStat")
library("phylotools")
library("stringr")

fas_dir <- file.path("~/Desktop/test")

fas_files <- list.files(path=fas_dir, pattern="*fasta")

list_df<-lapply(setNames(,fas_files), function(x,y,z,a) {
  y<-as.data.frame(phylotools::read.fasta(x))
  z<-stringr::str_split(y$seq.text, "")
  a<-data.frame(matrix(unlist(z), nrow=length(z), byrow=T))
  rownames(a)<-as.character(unlist(y[,1]))
  as.data.frame(t(a), row.names=F, stringsAsFactors=T)
})

PAC.vm<-compare_alignments (list_df[["HIVenv_valign_cut.fasta"]], 
                            list_df[["HIVenv_malign_cut.fasta"]])

plot_similarity_summary (PAC.vm, scale=TRUE, CS=FALSE, cys=FALSE, display=TRUE)