177 lines
No EOL
6 KiB
R
177 lines
No EOL
6 KiB
R
#logo plots
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# create functions
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# one with OR
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# --> select/drop down option to remove empty positions
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# --> easy peasy, just select the merged_df3_comp
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# --> select/drop down option for colour
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# --> if clustalx and taylor, set variable to black bg + white font
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# --> if chemistry and hydrophobicity, then grey bg + black font
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# --> select/drop down option for log scale
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# --> should include WT
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# one for multiple muts
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# --> select/drop down option to filter count of nsSNPs
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# --> select/drop down option for colour
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# --> should include WT
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# Data used
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#wide_df_or # or logo plot
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#wide_df_or_mult # > 1 sites
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#wide_df_logor_m #make it as a scale option. REDUNDANT
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#tab_mt # mutant logo plot
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#tab_wt # wt logo plot
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# Make it hover over position and then get the corresponding data table!
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#%%======================================================================
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#==================
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# logo data: OR
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#==================
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# NOTE: my_logo_col
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# Can be one of these: 'chemistry', 'hydrophobicity', 'clustalx', 'taylor'
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# if 'chemistry' or 'hydrophobicity' --> then bg is grey with black font (x, y and labels)
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# if 'clustalx'or 'taylor' --> then bg is black with white font (x, y and labels)
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#, theme_bgc =
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#, xfont_bgc =
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#, yfont_bgc =
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#, xtt_col =
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#, ytt_col =
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# ADD legend for hydrophobicity: done
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# ADD option to remove empty positions
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LogoPlotCustomH <- function(plot_df
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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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, rm_empty_pos = F
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, my_logo_col = "chemistry"
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, x_lab = "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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#, theme_bgc
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#, xfont_bgc
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#, yfont_bgc
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, y_ats = 22
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, y_tangle = 0
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, x_tts = 20 # title size
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, y_tts = 23
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#, xtt_col =
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#, ytt_col =
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, leg_pos = "none" # 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 = 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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# Data processing for logo plot
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#################################
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if (rm_empty_pos){
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plot_df = plot_df[!is.na(plot_df[y_axis_colname]),]
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cat("\nRemoving empty positions...\n")
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}else{
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plot_df = plot_df
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}
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#-------------------
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# logo data: LogOR
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#-------------------
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if (y_axis_log){
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log_colname = paste0("log_", y_axis_colname)
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plot_df[log_colname] = log_value(plot_df[y_axis_colname])
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logo_df = plot_df[, c(x_axis_colname, symbol_colname, log_colname)]
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logo_df_plot = logo_df[, c(x_axis_colname, symbol_colname, log_colname)]
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logo_dfP_wf = as.matrix(logo_df_plot %>% spread(x_axis_colname, log_colname, fill = 0.0))
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} else {
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#-------------------
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# logo data: OR
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#-------------------
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logo_df = plot_df[, c(x_axis_colname, symbol_colname, y_axis_colname)]
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logo_df_plot = logo_df[, c(x_axis_colname, symbol_colname, y_axis_colname)]
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logo_dfP_wf = as.matrix(logo_df_plot %>% spread(x_axis_colname, y_axis_colname, fill = 0.0))
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}
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class(logo_dfP_wf)
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rownames(logo_dfP_wf) = logo_dfP_wf[,1]
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dim(logo_dfP_wf)
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logo_dfP_wf = logo_dfP_wf[,-1]
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str(logo_dfP_wf)
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colnames(logo_dfP_wf)
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position_or = as.numeric(colnames(logo_dfP_wf))
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######################################
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# Generating plots with given y_axis
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#####################################
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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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, "\nUsing black theme\n")
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theme_bgc = "black"
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xfont_bgc = "white"
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yfont_bgc = "white"
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xtt_col = "white"
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ytt_col = "white"
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}
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if (my_logo_col %in% c('chemistry', 'hydrophobicity')) {
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cat('\nSelected colour scheme:', my_logo_col
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, "\nUsing grey theme")
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theme_bgc = "grey"
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xfont_bgc = "black"
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yfont_bgc = "black"
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xtt_col = "black"
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ytt_col = "black"
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}
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LogoPlot = ggseqlogo(logo_dfP_wf
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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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#ylab("my custom height") +
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theme(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_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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, 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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, 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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, legend.text = element_text(size = leg_ts)
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, legend.title = element_text(size = leg_tts))+
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scale_x_discrete(x_lab
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#, breaks
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, labels = position_or
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, limits = factor(1:length(position_or))) +
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ylab(y_lab)
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return(LogoPlot)
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} |