various stuff
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3 changed files with 99 additions and 76 deletions
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@ -34,7 +34,7 @@ ColourPalleteMulti = function(df, group, subgroup){
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# above function
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#########################
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bp_stability_hmap <- function(plotdf = merged_df3
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bp_stability_hmap <- function(plot_df = merged_df3
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, xvar_colname = "position"
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, yvar_colname = 'duet_scaled' #FIXME: temp, remove
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#, bar_col_colname = "group"
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@ -68,30 +68,30 @@ bp_stability_hmap <- function(plotdf = merged_df3
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# Build data with colours
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# ~ ligand distance
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#=========================
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plotdf = generate_distance_colour_map(plotdf, debug=TRUE)
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plot_df = generate_distance_colour_map(plot_df, debug=TRUE)
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# order the df by position and ensure it is a factor
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plotdf = plotdf[order(plotdf[[xvar_colname]]), ]
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plotdf[[xvar_colname]] = factor(plotdf[[xvar_colname]])
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plot_df = plot_df[order(plot_df[[xvar_colname]]), ]
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plot_df[[xvar_colname]] = factor(plot_df[[xvar_colname]])
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#cat("\nSneak peak:\n")
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head(data.frame( plotdf[[xvar_colname]], plotdf[[stability_colname]] ) )
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head(data.frame( plot_df[[xvar_colname]], plot_df[[stability_colname]] ) )
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# stability values isolated to help with generating column called: 'group'
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my_grp = plotdf[[stability_colname]]
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my_grp = plot_df[[stability_colname]]
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cat( "\nLength of nsSNPs:", length(my_grp)
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, "\nLength of unique values for nsSNPs:", length(unique(my_grp)) )
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# Add col: 'group'
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plotdf$group = paste0(plotdf[[stability_outcome_colname]], "_", my_grp, sep = "")
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plot_df$group = paste0(plot_df[[stability_outcome_colname]], "_", my_grp, sep = "")
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# check unique values in normalised data
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cat("\nNo. of unique values in", stability_colname, "no rounding:"
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, length(unique(plotdf[[stability_colname]])))
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, length(unique(plot_df[[stability_colname]])))
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# Call the function to create the palette based on the group defined above
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#subcols_ps
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subcols_bp_hmap = ColourPalleteMulti(plotdf, stability_outcome_colname, stability_colname)
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subcols_bp_hmap = ColourPalleteMulti(plot_df, stability_outcome_colname, stability_colname)
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cat("\nNo. of sub colours generated:", length(subcols_bp_hmap))
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@ -100,40 +100,54 @@ bp_stability_hmap <- function(plotdf = merged_df3
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# Generate the subcols barplot
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#-------------------------------
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cowplot::plot_grid(
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ggplot(plotdf, aes_string(x = xvar_colname
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# , ordered = T)
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ggplot(plot_df, aes_string(x = xvar_colname
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# , ordered = T)
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)) +
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geom_bar(aes(fill = group)
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, colour = "grey") +
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scale_fill_manual( values = subcols_bp_hmap
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, guide = "none") +
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# scale_x_discrete("Position", labels=factor(plot_df$position)) +
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theme( axis.text.x = element_text(size = my_xaxls
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, angle = 90
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, hjust = 1
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, vjust = 0.4)
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, axis.text.y = element_text(size = my_yaxls
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, angle = 0
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, hjust = 1
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, vjust = 0)
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, axis.title.x = element_text(size = my_xaxts)
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, axis.title.y = element_text(size = my_yaxts )
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, plot.title = element_text(size = my_pts
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, hjust = 0.5)) +
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theme(
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axis.text.x = element_text(size = my_xaxls
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, angle = 90
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, hjust = 1
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, vjust = 0.4)
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, axis.text.y = element_text(size = my_yaxls
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, angle = 0
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, hjust = 1
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, vjust = 0)
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, axis.title.x = element_blank()
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#, axis.title.x = element_text(size = my_xaxts)
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, axis.title.y = element_text(size = my_yaxts )
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, plot.title = element_text(size = my_pts
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, hjust = 0.5)) +
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labs(title = p_title
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, x = my_xlab
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, y = my_ylab),
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geom_tile(aes(, tpos0 # heat-mapped distance tiles along the bot
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, width = tW0
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, height = tH0)
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, fill = plotdf$ligD_colours
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, colour = plotdf$ligD_colours
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, linetype = "blank"), #end of distance-heat-bar
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generate_distance_legend(plotdf),
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ncol = 2,
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#align = "hv",
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rel_widths = c(9/10, 0.4/10)
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NULL,
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ggplot(plot_df,
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aes(x=factor(position), # THIS STUPID FUCKING FACTOR THING
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)
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) +
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geom_tile(aes(y=0),
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fill=plot_df$ligD_colours) +
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scale_x_discrete("Position", labels=factor(plot_df$position)) +
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theme_nothing() +
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theme(plot.background = element_rect(fill = "transparent", colour=NA),
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plot.margin = margin(t=0,b=0)) +
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labs(x = NULL, y = NULL), #end of distance-heat-bar
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NULL,
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position_annotation(plot_df),
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#generate_distance_legend(plot_df),
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ncol = 1,
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align = "v",
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rel_heights = c(10,-0.1,1,-0.1,1)
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#rel_widths = c(9/10, 0.4/10)
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)
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}
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bp_stability_hmap(small_df3)
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@ -250,64 +250,73 @@ LogoPlotSnps <- function(plot_df
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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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)
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,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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, plot.background = element_rect(fill = theme_bgc, colour=NA)
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),
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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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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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, labels = as.factor(colnames(tab_wt))) +
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theme(text = element_text(family="FreeSans")
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, legend.position = "none"
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, axis.text.x = element_blank()
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, axis.text.y = element_blank()
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, axis.title.x = element_blank()
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, axis.title.y = element_blank()
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, plot.background = element_rect(fill = theme_bgc)
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, plot.background = element_rect(fill = theme_bgc, colour=NA)
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) +
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labs(x=NULL, y=NULL)
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,
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ggplot(data=unique_colour_map2, aes(
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x=factor(position), 0 # heat-mapped distance tiles along the bot
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, fill = position
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, colour = position
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, linetype = "blank"
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)
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labs(x=NULL, y=NULL),
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ggplot(
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data=unique_colour_map2,
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aes(
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x=factor(position), 0 # heat-mapped distance tiles along the bot
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, fill = position
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, colour = position
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, linetype = "blank"
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)
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) +
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geom_tile() +
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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_blank()
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, axis.ticks.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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, 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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theme(
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axis.text.x = element_blank()
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, axis.ticks.x = element_blank()
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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.ticks.y = element_blank()
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, axis.title.x = element_blank()
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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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, plot.margin = margin(t=0)
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, panel.grid=element_blank()
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, panel.background = element_rect(fill = theme_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 = leg_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, colour=NA)
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, plot.margin = margin(t=0)
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, panel.grid=element_blank()
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, panel.background = element_rect(fill = theme_bgc, colour=NA)
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) +
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scale_x_discrete(x_lab, labels=factor(unique_colour_map$position)) +
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scale_color_manual(values=unique_colour_map$ligD_colours) +
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scale_fill_manual(values=unique_colour_map$ligD_colours) +
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labs(y = NULL)
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, nrow = 3
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, NULL
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, position_annotation(plot_df, bg=theme_bgc)
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, ncol=1
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, align = "v"
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, rel_heights = c(7/10, 2/7, 1/7))
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, rel_heights = c(7/10, 2/7,1/7, -0.1, 0.5/7))
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#------------------
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# Wild logo plot
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#------------------
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}
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#LogoPlotSnps(mutable_df3)
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#LogoPlotSnps(small_df3)
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@ -27,7 +27,7 @@ wideP_consurf2 <- function(plot_df
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, lower_EB_colname = "consurf_ci_lower"
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, plot_type = "point" # default is point
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, point_colours
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, point_colours = consurf_bp_colours
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, p_size = 2
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, leg_title1 = ""
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, leg_labels = c("0": "Insufficient Data"
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@ -321,7 +321,7 @@ wideP_consurf2 <- function(plot_df
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g1_leg = g1_leg + geom_bar(aes_string(fill = sprintf("factor(%s)"
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, yvar_colourN_colname)))
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g1_leg = g1_leg + scale_fill_manual(values = consurf_palette1 , name = leg_title1)
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g1_leg = g1_leg + scale_fill_manual(values = consurf_bp_colours , name = leg_title1)
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g1_leg
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legend1 = get_legend(g1_leg)
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