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tried ED logo, but needs work

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Tanushree Tunstall 2022-01-18 16:53:16 +00:00
parent 00094f036a
commit 8f8a9db92c
3 changed files with 119 additions and 108 deletions
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90
scripts/functions/logoP_msa.R
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@ -166,38 +166,42 @@ LogoPlotMSA <- function(msaSeq_mut
, method = msa_method
, col_scheme = my_logo_col
, seq_type = 'aa') +
scale_x_discrete(x_lab
, breaks = i_extract
, labels = i_extract
#, limits = min(i_extract): max(i_extract))
, limits = factor(i_extract))
# further customisation
msa_mut_logo_P = p0 + theme(legend.position = leg_pos
, legend.direction = leg_dir
#, legend.title = element_blank()
, legend.title = element_text(size = leg_tts
, colour = ytt_col)
, legend.text = element_text(size = leg_ts)
theme(legend.position = leg_pos
, legend.direction = leg_dir
#, legend.title = element_blank()
, legend.title = element_text(size = leg_tts
, colour = ytt_col)
, legend.text = element_text(size = leg_ts)
, axis.text.x = element_text(size = x_ats
, angle = x_tangle
, hjust = 1
, vjust = 0.4
, colour = xfont_bgc)
#, axis.text.y = element_blank()
, axis.text.y = element_text(size = y_ats
, angle = y_tangle
, hjust = 1
, vjust = -1.0
, colour = yfont_bgc)
, axis.title.x = element_text(size = x_tts
, colour = xtt_col)
, axis.title.y = element_text(size = y_tts
, colour = ytt_col)
, plot.background = element_rect(fill = theme_bgc))
, axis.text.x = element_text(size = x_ats
, angle = x_tangle
, hjust = 1
, vjust = 0.4
, colour = xfont_bgc)
#, axis.text.y = element_blank()
, axis.text.y = element_text(size = y_ats
, angle = y_tangle
, hjust = 1
, vjust = -1.0
, colour = yfont_bgc)
, axis.title.x = element_text(size = x_tts
, colour = xtt_col)
, axis.title.y = element_text(size = y_tts
, colour = ytt_col)
, plot.background = element_rect(fill = theme_bgc))+
xlab(x_lab)
if (missing(plot_positions)){
msa_mut_logo_P = p0
}else{
msa_mut_logo_P = p0 +
scale_y_continuous(expand = c(0,0.09)) +
scale_x_discrete(breaks = i_extract
, expand = c(0.09,0)
, labels = i_extract
, limits = factor(i_extract))
}
cat('\nDone: msa_mut_logo_P')
#return(msa_mut_logoP)
@ -210,15 +214,7 @@ LogoPlotMSA <- function(msaSeq_mut
, facet = "grid"
, method = msa_method
, col_scheme = my_logo_col
, seq_type = 'aa')+
scale_x_discrete(x_lab
, breaks = i_extract
, labels = i_extract
#, limits = min(i_extract): max(i_extract))
, limits = factor(i_extract))
# further customisation
msa_wt_logo_P = p1 +
, seq_type = 'aa') +
theme(legend.position = "none"
, legend.direction = leg_dir
@ -240,8 +236,20 @@ LogoPlotMSA <- function(msaSeq_mut
, colour = ytt_col)
, plot.background = element_rect(fill = theme_bgc)) +
ylab("")
ylab("") + xlab("Wild-type position")
if (missing(plot_positions)){
msa_wt_logo_P = p1
}else{
msa_wt_logo_P = p1 +
scale_y_continuous(expand = c(0,0.09)) +
scale_x_discrete(breaks = i2_extract
, expand = c(0.09,0)
, labels = i2_extract
, limits = factor(i2_extract))
}
cat('\nDone: msa_wt_logo_P')
#return(msa_wt_logoP)
LogoPlotMSAL[['msa_wt_logoP']] <- msa_wt_logo_P