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updated docs for the logo functions and tested all of them again

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Tanushree Tunstall 2022-01-26 15:53:53 +00:00
parent 2f7f40efb1
commit 7317156bba
5 changed files with 135 additions and 80 deletions
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42
scripts/functions/logoP_msa.R
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@ -1,8 +1,46 @@
#####################################################################################
# LogoPlotMSA():
# Input:
# Data:
# msaSeq_mut: MSA chr vector for muts
# msaSeq_wt: MSA chr vector for wt
# Logo type params:
# logo_type = c("EDLogo", "bits_pfm", "probability_pfm", "bits_raw", "probability_raw")
# EDLogo: calculated from the Logolas package based on PFM matrix (scaled).
#The required content from the package is sourced locally within 'my_logolas.R'
# bits_pfm: Information Content based on PFM scaled matrix (my_logolas.R)
# probability_pfm: Probability based on PFM scaled matrix (my_logolas.R)
# bits_raw: Information Content based on Raw MSA (ggseqlogo)
# probability_raw: Probability based on Raw MSA (ggseqlogo)
# EDScore_type = c("log", log-odds", "diff", "probKL", "ratio", "unscaled_log", "wKL")
# bg_prob: background probability, default is equal i.e NULL.
# This is used by the internal call to DataED_PFM(). This func takes thse args. I have used it here for
# completeness and allow nuanced plot control
# my_logo_col = c("chemistry", "hydrophobicity", "clustalx", "taylor")
# --> if clustalx and taylor, set variable to black bg + white font
# --> if chemistry and hydrophobicity, then grey bg + black font
# ...other params
# Returns: Logo plots from MSA both mutant and wt (for comparability)
# For my case, I always use it as it helps see what is at the wild-type already!
# TODO: SHINY
# drop down: logo_type
# drop down: ED score type
# drop down/enter field : bg probability (in the actual plot function!)
# drop down: my_logo_col
# Make it hover over position and then get the corresponding data table!
###################################################################################
###########################################
LogoPlotMSA <- function(msaSeq_mut # chr vector
, msaSeq_wt # chr vector
#, msa_method = c("custom") # can be "bits", "probability" or "custom"
, logo_type = c("EDLogo") #"bits_pfm", "probability_pfm", "bits_raw", "probability_raw") # can be "bits", "probability" or "custom"
, 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
, my_logo_col = "chemistry"