updated and tested logoP_snp.R. All done nicely
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0334188801
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4 changed files with 155 additions and 99 deletions
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@ -142,11 +142,11 @@ LogoPlotSnps <- function(plot_df
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, "\nRownames of mutant matrix:", rownames(tab_wt)
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, "\nColnames of mutant matrix:", colnames(tab_wt))
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}
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######################################
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# Generating plots with given y_axis
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# Generating plots for muts and wt
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#####################################
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LogoPlotL <- list()
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if (my_logo_col %in% c('clustalx','taylor')) {
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cat("\nSelected colour scheme:", my_logo_col
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@ -169,76 +169,132 @@ LogoPlotSnps <- function(plot_df
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xtt_col = "black"
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ytt_col = "black"
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}
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#LogoSnps_P
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mut_logo_p = ggseqlogo(tab_mt
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, method = "custom"
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, col_scheme = my_logo_col) +
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#####################################
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# Generating logo plots for nsSNPs
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#####################################
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#-------------------
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# Mutant logo plot
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#-------------------
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p0 = ggseqlogo(tab_mt
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, method = 'custom'
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, col_scheme = my_logo_col
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, seq_type = 'aa') +
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theme(
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# panel.grid = element_blank(),
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theme(text=element_text(family="FreeSans"))+
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theme(axis.text.x = element_blank()) +
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theme_logo()+
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# axis.text.x = element_text(size = x_ats
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# , angle = x_tangle
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# , hjust = 1
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# , vjust = 0.4
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# , colour = xfont_bgc)
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scale_x_continuous(breaks = 1:ncol(tab_mt)
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, expand = c(0.01,0)
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, labels = colnames(tab_mt))+
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scale_y_continuous(breaks = 0:(max_mult_mut-1)
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, labels = c(1:max_mult_mut)
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, limits = c(0, max_mult_mut)) +
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#xlab(x_lab) +
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ylab(y_lab)
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# , axis.text.y = element_text(size = y_ats
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# , angle = y_tangle
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# , hjust = 1
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# , vjust = 0
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# , colour = yfont_bgc)
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cat('\nDone: p0')
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# further customisation
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mut_logo_p <<- p0 + theme(legend.position = leg_pos
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, legend.direction = leg_dir
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#, legend.title = element_blank()
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, legend.title = element_text(size = y_tts
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, colour = ytt_col)
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, legend.text = element_text(size = leg_ts)
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, axis.title.x = element_text(size = x_tts
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, colour = xtt_col)
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, axis.text.x = element_text(size = x_ats
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, angle = x_tangle
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, hjust = 1
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, vjust = 0.4
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, colour = xfont_bgc)
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#, axis.text.y = element_blank()
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, axis.text.y = element_text(size = y_ats
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, angle = y_tangle
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, hjust = 1
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, vjust = -1.0
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, colour = yfont_bgc)
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, axis.title.x = element_text(size = x_tts
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, colour = xtt_col)
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, axis.title.y = element_text(size = y_tts
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, colour = ytt_col)
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, plot.background = element_rect(fill = theme_bgc))
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cat('\nDone: mut_logo_p')
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#return(mut_logo_p)
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LogoPlotL[['mut_logoP']] <- mut_logo_p
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, axis.title.y = element_text(size = y_tts
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, colour = ytt_col)
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#------------------
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# Wild logo plot
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#------------------
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p1 = ggseqlogo(tab_wt
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, method = 'custom'
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, col_scheme = my_logo_col
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, seq_type = 'aa') +
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theme(text = element_text(family="FreeSans"))+
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theme(axis.text.x = element_blank()
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, axis.text.y = element_blank()) +
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theme_logo()+
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scale_x_continuous(breaks = 1:ncol(tab_wt)
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, expand = c(0.01,0)
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, labels = colnames(tab_wt))+
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xlab(x_lab)
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cat('\nDone: p1')
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# further customisation
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wt_logo_p <<- p1 +
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theme(legend.position = "none"
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, legend.direction = leg_dir
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#, legend.title = element_blank()
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, legend.title = element_text(size = y_tts
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, colour = ytt_col)
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, legend.text = element_text(size = leg_ts)
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, legend.position = leg_pos
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, legend.direction = leg_dir
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, plot.background = element_rect(fill = theme_bgc))+
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#theme(text = element_text(family = "FreeSans"))+
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# theme_logo(base_size = 18)+
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# scale_x_continuous(breaks = 1:ncol(tab_mt)
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# , labels = colnames(tab_mt))+
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# scale_y_continuous(breaks = 1:max_mult_mut
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# , limits = c(0, max_mult_mut)) +
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scale_x_discrete(x_lab
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, labels = colnames(tab_mt)
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, limits = factor(1:ncol(tab_mt)))+
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scale_y_continuous(y_lab
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, breaks = 1:max_mult_mut
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, limits = c(0, max_mult_mut))#+
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# ylab(y_lab)+xlab(x_lab)
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, axis.text.x = element_text(size = x_ats
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, angle = x_tangle
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, hjust = 1
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, vjust = 0.4
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, colour = xfont_bgc)
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, axis.text.y = element_blank()
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, axis.title.x = element_text(size = x_tts
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, colour = xtt_col)
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, axis.title.y = element_text(size = y_tts
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, colour = ytt_col)
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, plot.background = element_rect(fill = theme_bgc))
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cat('\nDone: wt_logo_p')
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#return(wt_logo_p)
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LogoPlotL[['wt_logoP']] <- wt_logo_p
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#=========================================
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# Output
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# Combined plot: logo_mutliple_muts.svg
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#=========================================
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#suppressMessages( require(cowplot) )
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#plot_grid(p1, p3, ncol = 1, align = 'v')
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cat('\nDone: mut_logo_p + wt_logo_p')
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return(mut_logo_p)
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# colour scheme: https://rdrr.io/cran/ggseqlogo/src/R/col_schemes.r
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#cat("\nOutput plot:", LogoSNPs_comb, "\n")
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#svg(LogoSNPs_combined, width = 32, height = 10)
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LogoPlotL[['wt_logoP']] <- wt_logo_p
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LogoSNPs_comb = cowplot::plot_grid(LogoPlotL[['mut_logoP']]
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, LogoPlotL[['wt_logoP']]
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, nrow = 2
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, align = "v"
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, rel_heights = c(3/4, 1/4))
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return(LogoSNPs_comb)
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}
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LogoPlotSnps(plot_df = merged_df3
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, x_axis_colname = "position"
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, symbol_mut_colname = "mutant_type"
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, symbol_wt_colname = "mutant_type"
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, omit_snp_count = c(0)# can be 1, 2, etc.
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, my_logo_col = "chemistry"
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, x_lab = "Position"
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, y_lab = "Count"
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, x_ats = 1 # text size
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, x_tangle = 90 # text angle
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, y_ats = 1
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, y_tangle = 0
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, x_tts = 20 # title size
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, y_tts = 20
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, leg_pos = "top" # can be top, left, right and bottom or c(0.8, 0.9)
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, leg_dir = "horizontal" #can be vertical or horizontal
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, leg_ts = 20 # leg text size
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, leg_tts = 16 # leg title size
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)
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@ -6,20 +6,19 @@
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LogoPlotSnps(plot_df = merged_df3
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, x_axis_colname = "position"
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, symbol_mut_colname = "mutant_type"
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, symbol_wt_colname = "mutant_type"
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, symbol_wt_colname = "wild_type"
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, omit_snp_count = c(0)# can be 1, 2, etc.
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, my_logo_col = "chemistry"
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, x_lab = "Position"
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, y_lab = "Count"
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, x_ats = 1 # text size
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, my_logo_col = "taylor"
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, x_lab = "Wild-type position"
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, y_lab = ""
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, x_ats = 13 # text size
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, x_tangle = 90 # text angle
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, y_ats = 1
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, y_ats = 20
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, y_tangle = 0
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, x_tts = 20 # title size
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, y_tts = 20
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, x_tts = 18 # title size
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, y_tts = 18
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, leg_pos = "top" # can be top, left, right and bottom or c(0.8, 0.9)
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, leg_dir = "horizontal" #can be vertical or horizontal
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, leg_ts = 20 # leg text size
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, leg_ts = 14 # leg text size
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, leg_tts = 16 # leg title size
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)
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