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added a few tweaks to check logoplots

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Tanushree Tunstall 2022-01-26 15:22:13 +00:00
parent 1b20f09075
commit 2f7f40efb1
2 changed files with 8 additions and 9 deletions
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7
scripts/functions/logoP_msa.R
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@ -57,7 +57,7 @@ LogoPlotMSA <- function(msaSeq_mut # chr vector
cat("\nY-axis lower limit:", ylim_low)
y_rlow = seq(0, ylim_low, length.out = 3); y_rlow
ylim_up <- ceiling(max(data_logo_mut)) + 4; ylim_up
ylim_up <- ceiling(max(data_logo_mut)) + 5; ylim_up
cat("\nY-axis upper limit:", ylim_up)
y_rup = seq(0, ylim_up, by = 2); y_rup
}else{
@ -185,9 +185,7 @@ LogoPlotMSA <- function(msaSeq_mut # chr vector
, "\nFiltering positions as specified..."
, "\nNo. of positions in plot:", length(plot_positions))
i_extract = plot_positions
#plot_mut_edM = data_logo_mut[, i_extract]
#plot_wt_edM = data_logo_wt[, i_extract]
#-----------------
# PFM: mut + wt
#------------------
@ -195,6 +193,7 @@ LogoPlotMSA <- function(msaSeq_mut # chr vector
plot_mut_edM = data_logo_mut[, i_extract]
plot_wt_edM = data_logo_wt[, i_extract]
}
if (logo_type%in%c("bits_raw", "probability_raw")){