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2 changed files with 73 additions and 94 deletions
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@ -47,13 +47,14 @@ LogoPlotMSA <- function(unified_msa
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, my_logo_col = "chemistry"
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, my_logo_col = "chemistry"
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, plot_positions
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, plot_positions
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, y_breaks
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, y_breaks
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, x_lab_mut = "nsSNP-position"
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, x_lab_mut = "nsSNP position"
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, y_lab_mut
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, y_lab_mut
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, x_ats = 13 # text size
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, x_ats = 13 # text size
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, x_tangle = 90 # text angle
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, x_tangle = 90 # text angle
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, x_axis_offset = 0.05 # dist b/w y-axis and plot start
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, x_axis_offset = 0 # dist b/w y-axis and plot start
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, x_axis_offset_filtered = 0.2
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, x_axis_offset_filtered = 0
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, y_axis_offset = 0.05
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, y_axis_offset = 0
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, y_axis_increment = 1
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, y_ats = 13
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, y_ats = 13
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, y_tangle = 0
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, y_tangle = 0
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, x_tts = 13 # title size
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, x_tts = 13 # title size
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@ -102,7 +103,7 @@ LogoPlotMSA <- function(unified_msa
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y_rlow = seq(0, ylim_low, length.out = 3); y_rlow
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y_rlow = seq(0, ylim_low, length.out = 3); y_rlow
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ylim_up <- ceiling(max(data_logo_mut)) + 5; ylim_up
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ylim_up <- ceiling(max(data_logo_mut)) + 5; ylim_up
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cat("\nY-axis upper limit:", ylim_up)
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cat("\nY-axis upper limit:", ylim_up)
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y_rup = seq(0, ylim_up, by = 2); y_rup
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y_rup = seq(0, ylim_up, by = 2); y_rup
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}else{
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}else{
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ylim_low = ylim_low + (-0.5)
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ylim_low = ylim_low + (-0.5)
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@ -192,7 +193,7 @@ LogoPlotMSA <- function(unified_msa
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#---------
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#---------
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# MSA mut
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# MSA mut
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#---------
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#---------
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cat("\n==========================================="
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cat("\n==========================================="
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, "\nGenerated PFM mut: No filtering"
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, "\nGenerated PFM mut: No filtering"
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, "\n===========================================")
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, "\n===========================================")
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@ -301,7 +302,7 @@ LogoPlotMSA <- function(unified_msa
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, '\nSelected colour scheme:', my_logo_col
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, '\nSelected colour scheme:', my_logo_col
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, "\nUsing grey theme")
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, "\nUsing grey theme")
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theme_bgc = "grey"
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theme_bgc = "white"
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xfont_bgc = "black"
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xfont_bgc = "black"
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yfont_bgc = "black"
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yfont_bgc = "black"
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xtt_col = "black"
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xtt_col = "black"
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@ -317,10 +318,10 @@ LogoPlotMSA <- function(unified_msa
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#-------------------
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#-------------------
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# Mutant logo plot
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# Mutant logo plot
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#-------------------
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#-------------------
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p0 = ggseqlogo(plot_mut_edM
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p0 = ggplot() + geom_logo(plot_mut_edM
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, method = msa_method
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, method = msa_method
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, col_scheme = my_logo_col
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, col_scheme = my_logo_col
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, seq_type = 'auto') +
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, seq_type = 'auto') +
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theme(legend.position = leg_pos
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theme(legend.position = leg_pos
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, legend.direction = leg_dir
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, legend.direction = leg_dir
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@ -335,6 +336,7 @@ LogoPlotMSA <- function(unified_msa
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, vjust = 0.4
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, vjust = 0.4
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, colour = xfont_bgc)
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, colour = xfont_bgc)
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#, axis.text.y = element_blank()
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#, axis.text.y = element_blank()
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, axis.ticks=element_blank()
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, axis.text.y = element_text(size = y_ats
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, axis.text.y = element_text(size = y_ats
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, angle = y_tangle
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, angle = y_tangle
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, hjust = 1
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, hjust = 1
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@ -344,12 +346,24 @@ LogoPlotMSA <- function(unified_msa
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, colour = xtt_col)
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, colour = xtt_col)
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, axis.title.y = element_text(size = y_tts
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, axis.title.y = element_text(size = y_tts
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, colour = ytt_col)
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, colour = ytt_col)
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, plot.background = element_rect(fill = theme_bgc)) +
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, panel.grid=element_blank()
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, plot.background = element_rect(fill = theme_bgc, colour=NA)
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, panel.background = element_rect(fill = "transparent", colour=NA)
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) +
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labs(y=y_label) +
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xlab(x_lab_mut)
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xlab(x_lab_mut)
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if (missing(plot_positions)){
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if (missing(plot_positions)){
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ed_mut_logo_P = p0 +
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ed_mut_logo_P = p0 +
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scale_y_continuous(
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expand = c(0,0),
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breaks = seq(
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0,
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(y_lim),
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by = y_axis_increment
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)
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) +
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scale_x_discrete(breaks = msa_pos
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scale_x_discrete(breaks = msa_pos
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, expand = c(x_axis_offset, 0)
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, expand = c(x_axis_offset, 0)
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, labels = msa_pos
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, labels = msa_pos
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@ -357,55 +371,37 @@ LogoPlotMSA <- function(unified_msa
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}else{
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}else{
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ed_mut_logo_P = p0 +
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ed_mut_logo_P = p0 +
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scale_y_continuous(
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expand = c(0,0)#,
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# breaks = seq(
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# 0,
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# (y_lim),
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# by = y_axis_increment
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#)
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) +
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# scale_x_continuous(expand = c(0,0)) #+
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scale_x_discrete(breaks = i_extract
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scale_x_discrete(breaks = i_extract
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, expand = c(x_axis_offset_filtered, 0)
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, expand = c(x_axis_offset_filtered, 0)
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, labels = i_extract
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, labels = i_extract
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, limits = factor(i_extract))
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, limits = factor(i_extract))
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}
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if (logo_type == "EDLogo"){
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ed_mut_logo_P = ed_mut_logo_P +
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scale_y_continuous(limits = c(ylim_low, ylim_up)
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, breaks = ylim_scale
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, expand = c(0, y_axis_offset)) +
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geom_hline(yintercept = 0
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, linetype = "solid"
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, color = "grey"
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, size = 1)
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}
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if (missing(y_lab_mut)){
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ed_mut_logo_P = ed_mut_logo_P + ylab(y_label)
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} else{
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ed_mut_logo_P = ed_mut_logo_P + ylab(y_lab_mut)
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}
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}
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cat('\nDone: MSA plot for mutations')
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cat('\nDone: MSA plot for mutations')
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#return(msa_mut_logoP)
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#### Wild-type MSA: gene_fasta file ####
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PlotlogolasL[['ed_mut_logoP']] <- ed_mut_logo_P
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p1 = ggplot() + geom_logo(plot_wt_edM
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#, facet = "grid"
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#---------------------------------
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, method = msa_method
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# Wild-type MSA: gene_fasta file
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, col_scheme = my_logo_col
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#---------------------------------
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, seq_type = 'aa') +
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p1 = ggseqlogo(plot_wt_edM
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#, facet = "grid"
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, method = msa_method
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, col_scheme = my_logo_col
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, seq_type = 'aa') +
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theme(legend.position = "none"
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theme(legend.position = "none"
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, legend.direction = leg_dir
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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 = leg_tts
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, legend.title = element_text(size = leg_tts
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, colour = ytt_col)
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, colour = ytt_col)
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, legend.text = element_text(size = leg_ts)
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, legend.text = element_text(size = leg_ts)
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, axis.text.x = element_blank()
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, axis.text.x = element_text(size = x_ats
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, axis.ticks=element_blank()
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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_blank()
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, axis.title.x = element_text(size = x_tts
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, axis.title.x = element_text(size = x_tts
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@ -413,51 +409,34 @@ LogoPlotMSA <- function(unified_msa
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, axis.title.y = element_text(size = y_tts
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, axis.title.y = element_text(size = y_tts
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, colour = ytt_col)
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, colour = ytt_col)
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, plot.background = element_rect(fill = theme_bgc)) +
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, panel.grid=element_blank()
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, plot.background = element_rect(fill = theme_bgc, colour=NA)
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, panel.background = element_rect(fill = "transparent", colour=NA)
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, plot.margin = margin(r=0,l=0, unit="pt")
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) +
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scale_y_discrete(expand = c(0,0)) +
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ylab("") + xlab("Wild-type position")
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ylab("") + xlab("Wild-type position")
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if (missing(plot_positions)){
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if (missing(plot_positions)){
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# No y-axis needed
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# No y-axis needed
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ed_wt_logo_P = p1 +
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ed_wt_logo_P = p1# +
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scale_x_discrete(breaks = wt_pos
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, expand = c(x_axis_offset, 0)
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, labels = wt_pos
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, limits = factor(wt_pos))
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}else{
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}else{
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ed_wt_logo_P = p1 +
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ed_wt_logo_P = p1 +
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scale_x_discrete(breaks = i_extract
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scale_x_discrete(expand = c(0, 0),
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, expand = c(x_axis_offset_filtered, 0)
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breaks = i_extract,
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, labels = i_extract
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#labels = i_extract,
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, limits = factor(i_extract))
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limits = factor(i_extract)
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)
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}
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}
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cowplot::plot_grid(ed_mut_logo_P
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cat('\nDone: MSA plot for WT')
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, ed_wt_logo_P
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#return(msa_wt_logoP)
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, nrow = 2
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PlotlogolasL[['ed_wt_logoP']] <- ed_wt_logo_P
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, align = "v"
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#, axis='lr'
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#=========================================
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, rel_heights = c(3/4, 1/4))
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# Output
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# Combined plot: logo ED/other logo plot
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# customised for ggseqlogo
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#=========================================
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cat('\nDone: ed_mut_logoP + ed_wt_logoP')
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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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LogoED_comb = cowplot::plot_grid(PlotlogolasL[['ed_mut_logoP']]
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, PlotlogolasL[['ed_wt_logoP']]
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, nrow = 2
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, align = "v"
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, axis='lr'
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, rel_heights = c(3/4, 1/4))
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return(LogoED_comb)
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}
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}
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#LogoPlotMSA(unified_msa)
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#LogoPlotMSA(unified_msa)
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@ -48,7 +48,7 @@ site_snp_count_bp <- function (plotdf
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#-------------------------------------------
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#-------------------------------------------
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# adding column: snpcount for each position
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# adding column: snpcount for each position
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#-------------------------------------------
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#-------------------------------------------
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#setDT(plotdf)[, pos_count_check := .N, by = .(eval(parse(text = df_colname)))]
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#setDT(plotdf)[, position_count_check := .N, by = .(eval(parse(text = df_colname)))]
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# from dplyr
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# from dplyr
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plotdf = plotdf %>%
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plotdf = plotdf %>%
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@ -57,21 +57,21 @@ site_snp_count_bp <- function (plotdf
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plotdf = as.data.frame(plotdf)
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plotdf = as.data.frame(plotdf)
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class(plotdf)
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class(plotdf)
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nc_change = which(colnames(plotdf) == "n")
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nc_change = which(colnames(plotdf) == "n")
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colnames(plotdf)[nc_change] <- "pos_count"
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colnames(plotdf)[nc_change] <- "position_count"
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class(plotdf)
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class(plotdf)
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# if (all(plotdf$pos_count==plotdf$pos_count_check) ){
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# if (all(plotdf$position_count==plotdf$position_count_check) ){
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# cat("\nPASS: pos_count column created")
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# cat("\nPASS: position_count column created")
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# plotdf = plotdf[, !colnames(plotdf)%in%c("pos_count_check")]
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# plotdf = plotdf[, !colnames(plotdf)%in%c("position_count_check")]
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# }else{
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# }else{
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# stop("\nAbort: pos count numbes mismatch from dplyr and data.table")
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# stop("\nAbort: pos count numbes mismatch from dplyr and data.table")
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# }
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# }
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cat("\nCumulative nssnp count\n"
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cat("\nCumulative nssnp count\n"
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, table(plotdf$pos_count))
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, table(plotdf$position_count))
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# calculating total no. of mutations
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# calculating total no. of mutations
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tot_muts = sum(table(plotdf$pos_count))
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tot_muts = sum(table(plotdf$position_count))
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# sanity check
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# sanity check
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@ -92,10 +92,10 @@ site_snp_count_bp <- function (plotdf
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# creating df: average count of snpcount for each position
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# creating df: average count of snpcount for each position
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# created in earlier step
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# created in earlier step
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#-------------------------------------------------------
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#-------------------------------------------------------
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# use group by on pos_count
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# use group by on position_count
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snpsBYpos_df <- plotdf %>%
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snpsBYpos_df <- plotdf %>%
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dplyr::group_by(eval(parse(text = df_colname))) %>%
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dplyr::group_by(eval(parse(text = df_colname))) %>%
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dplyr::summarise(snpsBYpos = mean(pos_count)) # changed from summarize!
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dplyr::summarise(snpsBYpos = mean(position_count)) # changed from summarize!
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cat("\nnssnp count per position\n"
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cat("\nnssnp count per position\n"
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, table(snpsBYpos_df$snpsBYpos)
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, table(snpsBYpos_df$snpsBYpos)
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