tanu/LSHTM_analysis
1
0
Fork 0
Code Issues Pull requests Releases Wiki Activity

combined msa and wt seq into 1 list so only list is passed as an arg for plotting ED plots

Browse source
This commit is contained in:
Tanushree Tunstall 2022-02-15 08:31:58 +00:00
parent d38521e03a
commit 2274f01f23
5 changed files with 20 additions and 5 deletions
Download patch file Download diff file Expand all files Collapse all files

12
scripts/functions/logoP_msa.R
View file

@ -38,8 +38,9 @@
###########################################
LogoPlotMSA <- function(msaSeq_mut # chr vector
, msaSeq_wt # chr vector
#LogoPlotMSA <- function(msaSeq_mut # chr vector
# , msaSeq_wt # chr vector
LogoPlotMSA <- function(unified_msa
, logo_type = c("EDLogo") #"bits_pfm", "probability_pfm", "bits_raw", "probability_raw")
, EDScore_type = c("log") # see if this relevant, or source function should have it!
, bg_prob = NULL
@ -64,7 +65,12 @@ LogoPlotMSA <- function(msaSeq_mut # chr vector
)
{
# FIXME: Hack!
# msaSeq_mut=unified_msa[[1]]
# msaSeq_wt=unified_msa[[2]]
msaSeq_mut=unified_msa[['msa_seq']]
msaSeq_wt=unified_msa[['wt_seq']]
# Get PFM matrix for mut and wt MSA provided
data_ed = DataED_PFM(msaSeq_mut
, msaSeq_wt