tried ED logo, but needs work
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3 changed files with 119 additions and 108 deletions
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@ -166,38 +166,42 @@ LogoPlotMSA <- function(msaSeq_mut
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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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scale_x_discrete(x_lab
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, breaks = i_extract
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, labels = i_extract
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#, limits = min(i_extract): max(i_extract))
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, limits = factor(i_extract))
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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 = leg_tts
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, colour = ytt_col)
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, legend.text = element_text(size = leg_ts)
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# further customisation
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msa_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 = leg_tts
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, colour = ytt_col)
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, legend.text = element_text(size = leg_ts)
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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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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.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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if (missing(plot_positions)){
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msa_mut_logo_P = p0
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}else{
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msa_mut_logo_P = p0 +
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scale_y_continuous(expand = c(0,0.09)) +
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scale_x_discrete(breaks = i_extract
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, expand = c(0.09,0)
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, labels = i_extract
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, limits = factor(i_extract))
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}
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cat('\nDone: msa_mut_logo_P')
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#return(msa_mut_logoP)
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@ -210,15 +214,7 @@ LogoPlotMSA <- function(msaSeq_mut
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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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scale_x_discrete(x_lab
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, breaks = i_extract
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, labels = i_extract
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#, limits = min(i_extract): max(i_extract))
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, limits = factor(i_extract))
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# further customisation
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msa_wt_logo_P = p1 +
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, seq_type = 'aa') +
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theme(legend.position = "none"
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, legend.direction = leg_dir
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@ -240,7 +236,19 @@ LogoPlotMSA <- function(msaSeq_mut
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, colour = ytt_col)
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, plot.background = element_rect(fill = theme_bgc)) +
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ylab("")
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ylab("") + xlab("Wild-type position")
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if (missing(plot_positions)){
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msa_wt_logo_P = p1
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}else{
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msa_wt_logo_P = p1 +
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scale_y_continuous(expand = c(0,0.09)) +
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scale_x_discrete(breaks = i2_extract
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, expand = c(0.09,0)
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, labels = i2_extract
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, limits = factor(i2_extract))
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}
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cat('\nDone: msa_wt_logo_P')
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#return(msa_wt_logoP)
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@ -7,83 +7,84 @@ source("~/git/LSHTM_analysis/config/gid.R")
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# source("~/git/LSHTM_analysis/config/katg.R")
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# source("~/git/LSHTM_analysis/config/rpob.R")
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#---------------------------------------------------
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source("~/git/LSHTM_analysis/scripts/plotting/get_plotting_dfs.R")
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################################
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# Logo plot with custom Y axis
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# mainly OR
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# script: logoP.R
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################################
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LogoPlotCustomH (plot_df = merged_df3
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, x_axis_colname = "position"
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, y_axis_colname = "or_mychisq"
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, symbol_colname = "mutant_type"
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, y_axis_log = F
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, log_value = log10
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, y_axis_increment = 5
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, rm_empty_y = F
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, my_logo_col = 'chemistry'
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, x_lab = "Wild-type position"
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, y_lab = "Odds Ratio"
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, x_ats = 12 # text size
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, x_tangle = 90 # text angle
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, y_ats = 22
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, y_tangle = 0
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, x_tts = 19 # title size
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, y_tts = 22
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#, leg_pos = c(0.05,-0.12)
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, leg_pos = "top"
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, leg_dir = "horizontal"
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, leg_ts = 15 # leg text size
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, leg_tts = 16 # leg title size
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)
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########################################
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# Logo plot showing nsSNPs by positions
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# wild-type and mutant aa
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# script: logoP_snp.R
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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 = "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 = "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 = 20
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, y_tangle = 0
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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 = 14 # leg text size
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, leg_tts = 16 # leg title size
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)
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#source("~/git/LSHTM_analysis/scripts/plotting/get_plotting_dfs.R")
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#
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# ################################
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# # Logo plot with custom Y axis
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# # mainly OR
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# # script: logoP.R
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# ################################
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# LogoPlotCustomH (plot_df = merged_df3
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# , x_axis_colname = "position"
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# , y_axis_colname = "or_mychisq"
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# , symbol_colname = "mutant_type"
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# , y_axis_log = F
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# , log_value = log10
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# , y_axis_increment = 5
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# , rm_empty_y = F
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# , my_logo_col = 'chemistry'
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# , x_lab = "Wild-type position"
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# , y_lab = "Odds Ratio"
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# , x_ats = 12 # text size
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# , x_tangle = 90 # text angle
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# , y_ats = 22
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# , y_tangle = 0
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# , x_tts = 19 # title size
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# , y_tts = 22
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# #, leg_pos = c(0.05,-0.12)
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# , leg_pos = "top"
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# , leg_dir = "horizontal"
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# , leg_ts = 15 # leg text size
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# , leg_tts = 16 # leg title size
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# )
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#
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#
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# # ########################################
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# # # Logo plot showing nsSNPs by positions
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# # # wild-type and mutant aa
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# # # script: logoP_snp.R
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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 = "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 = "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 = 20
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# , y_tangle = 0
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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 = 14 # leg text size
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# , leg_tts = 16 # leg title size
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# )
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#
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#
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########################################
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# Logo plot MSA
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# Mutant and wild-type
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# wild-type and mutant aa
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# Can select active site residues
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# specify {plot_positions}
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# To plot entire MSA, simply don't specify {plot_positions}
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# script: logoP_msa.R
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########################################
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# BOTH WORK
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#LogoPlotMSA(msa_seq, wt_seq)
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# TODO perhaps: ED logo from Logolas
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########################################
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LogoPlotMSA(msaSeq_mut = msa_seq
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, msaSeq_wt = wt_seq
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, msa_method = 'bits' # or probability
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, my_logo_col = "chemistry"
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, my_logo_col = "taylor"
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#, plot_positions = active_aa_pos
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, plot_positions
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, x_lab = "Wild-type position"
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, x_lab = "nsSNP position"
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, y_lab = ""
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, x_ats = 13 # text size
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, x_ats = 10 # text size
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, x_tangle = 90 # text angle
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, y_ats = 13
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, y_tangle = 0
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@ -38,7 +38,9 @@ head(msa_seq)
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# fasta file: wt
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#================
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in_filename_fasta = paste0(tolower(gene), ".1fasta")
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#in_filename_fasta = paste0(tolower(gene), ".1fasta")
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in_filename_fasta = paste0(tolower(gene), "2.2fasta") # gid
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infile_fasta = paste0(indir, "/", in_filename_fasta)
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cat("\nInput fasta file for WT: ", infile_fasta, "\n")
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