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going through functions and script for interactive plots

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This commit is contained in:
Tanushree Tunstall 2022-01-12 17:58:16 +00:00
parent 1f266c4cb8
commit 3f7bc908ec
7 changed files with 83 additions and 95 deletions
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37
scripts/plotting/logo_plots.R
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@ -56,6 +56,8 @@ logo_combined_labelled = "logo_combined_labelled.svg"
plot_logo_combined_labelled = paste0(plotdir,"/", logo_combined_labelled)
#########################################################
#logo_or_mult_p + theme_dark()
#logo_or_mult_p + theme(plot.background = element_rect(fill = "black"))
#==================================
# Output
@ -124,8 +126,24 @@ print(logo_logOR)
#*****************************
# Mutant logo plot: >1 nsSNP
#******************************
aa_col_choices = c('chemistry', 'hydrophobicity', 'clustalx', 'taylor')
my_logo_col = aa_col_choices[[1]]
if (my_logo_col == 'clustalx || taylor'){
cat("\nSelected colour scheme:", my_logo_col
, "\nUsing black theme\n")
theme_bgc = "black"
font_bgc = "white"
} if (my_logo_col == 'chemistry || hydrophobicity') {
cat('\nSelected colour scheme:', my_logo_col
, "\nUsing grey theme")
theme_bgc = "grey"
font_bgc = "black"
}
p0 = ggseqlogo(tab_mt
, method = 'custom'
, col_scheme = my_logo_col
, seq_type = 'aa') +
#ylab('my custom height') +
theme(axis.text.x = element_blank()) +
@ -143,9 +161,12 @@ cat('\nDone: p0')
mut_logo_p = p0 + theme(legend.position = "none"
, legend.title = element_blank()
, legend.text = element_text(size = 20)
, axis.text.x = element_text(size = 14, angle = 90)
, axis.text.y = element_blank())
#mut_logo_p
, axis.text.x = element_text(size = 14
, angle = 90
, colour = font_bgc)
, axis.text.y = element_blank()
, plot.background = element_rect(fill = theme_bgc))
mut_logo_p
cat('\nDone: p0+mut_logo_p')
#*************************
@ -154,9 +175,7 @@ cat('\nDone: p0+mut_logo_p')
p2 = ggseqlogo(tab_wt
, method = 'custom'
, seq_type = 'aa'
#, col_scheme = "taylor"
#, col_scheme = chemistry2
) +
, col_scheme = my_logo_col) +
#ylab('my custom height') +
theme(text=element_text(family="FreeSans"))+
theme(axis.text.x = element_blank()
@ -185,7 +204,11 @@ cat('\nDone: wt_logo_p')
#***********************
# Logo OR >1 nsSNP
#***********************
logo_or_mult_p = ggseqlogo(wide_df_or_mult, method="custom", seq_type="aa") + ylab("my custom height") +
logo_or_mult_p = ggseqlogo(wide_df_or_mult
, method = "custom"
, col_scheme = my_logo_col
, seq_type="aa") +
ylab("my custom height") +
theme(axis.text.x = element_text(size = 14
, angle = 90
, hjust = 1