104 lines
4.2 KiB
R
Executable file
104 lines
4.2 KiB
R
Executable file
#########################################################
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# 1b: Define function: coloured barplot by subgroup
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# LINK: https://stackoverflow.com/questions/49818271/stacked-barplot-with-colour-gradients-for-each-bar
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#########################################################
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ColourPalleteMulti = function(df, group, subgroup){
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# Find how many colour categories to create and the number of colours in each
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categories <- aggregate(as.formula(paste(subgroup, group, sep="~" ))
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, df
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, function(x) length(unique(x)))
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# return(categories) }
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category.start <- (scales::hue_pal(l = 100)(nrow(categories))) # Set the top of the colour pallete
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category.end <- (scales::hue_pal(l = 40)(nrow(categories))) # set the bottom
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#return(category.start); return(category.end)}
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# Build Colour pallette
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colours <- unlist(lapply(1:nrow(categories),
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function(i){
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colorRampPalette(colors = c(category.start[i]
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, category.end[i]))(categories[i,2])}))
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return(colours)
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}
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#########################################################################
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bp_stability_hmap <- function(plotdf = merged_df3
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, xvar_colname = "position"
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#, bar_col_colname = "group"
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, stability_colname = "duet_scaled"
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, stability_outcome_colname = "duet_outcome"
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, p_title = "" # "Protein stability (DUET)"
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, my_xaxls = 12 # x-axis label size
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, my_yaxls = 20 # y-axis label size
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, my_xaxts = 18 # x-axis text size
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, my_yaxts = 20 # y-axis text size
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, my_pts = 20 # plot-title size
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, my_xlab = "Position"
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, my_ylab = "No. of nsSNPs"
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)
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{
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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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#cat("\nSneak peak:\n")
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head(data.frame( plotdf[[xvar_colname]], plotdf[[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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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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# 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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# 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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cat("\nNo. of sub colours generated:", length(subcols_bp_hmap))
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#-------------------------------
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# Generate the subcols barplot
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#-------------------------------
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#g = ggplot(plotdf, aes(x = factor(position, ordered = T)))
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g = ggplot(plotdf, aes_string(x = xvar_colname
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# , ordered = T)
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))
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OutWidePlot = g + 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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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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labs(title = p_title
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, x = my_xlab
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, y = my_ylab)
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return(OutWidePlot)
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}
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