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various stuff

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Tanushree Tunstall 2022-08-09 19:42:20 +01:00
parent 5cbaef3d36
commit 415d05ab6e
3 changed files with 99 additions and 76 deletions
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80
scripts/functions/bp_subcolours.R
View file

@ -34,7 +34,7 @@ ColourPalleteMulti = function(df, group, subgroup){
# above function # above function
######################### #########################
bp_stability_hmap <- function(plotdf = merged_df3 bp_stability_hmap <- function(plot_df = merged_df3
, xvar_colname = "position" , xvar_colname = "position"
, yvar_colname = 'duet_scaled' #FIXME: temp, remove , yvar_colname = 'duet_scaled' #FIXME: temp, remove
#, bar_col_colname = "group" #, bar_col_colname = "group"
@ -68,30 +68,30 @@ bp_stability_hmap <- function(plotdf = merged_df3
# Build data with colours # Build data with colours
# ~ ligand distance # ~ ligand distance
#========================= #=========================
plotdf = generate_distance_colour_map(plotdf, debug=TRUE) plot_df = generate_distance_colour_map(plot_df, debug=TRUE)
# order the df by position and ensure it is a factor # order the df by position and ensure it is a factor
plotdf = plotdf[order(plotdf[[xvar_colname]]), ] plot_df = plot_df[order(plot_df[[xvar_colname]]), ]
plotdf[[xvar_colname]] = factor(plotdf[[xvar_colname]]) plot_df[[xvar_colname]] = factor(plot_df[[xvar_colname]])
#cat("\nSneak peak:\n") #cat("\nSneak peak:\n")
head(data.frame( plotdf[[xvar_colname]], plotdf[[stability_colname]] ) ) head(data.frame( plot_df[[xvar_colname]], plot_df[[stability_colname]] ) )
# stability values isolated to help with generating column called: 'group' # stability values isolated to help with generating column called: 'group'
my_grp = plotdf[[stability_colname]] my_grp = plot_df[[stability_colname]]
cat( "\nLength of nsSNPs:", length(my_grp) cat( "\nLength of nsSNPs:", length(my_grp)
, "\nLength of unique values for nsSNPs:", length(unique(my_grp)) ) , "\nLength of unique values for nsSNPs:", length(unique(my_grp)) )
# Add col: 'group' # Add col: 'group'
plotdf$group = paste0(plotdf[[stability_outcome_colname]], "_", my_grp, sep = "") plot_df$group = paste0(plot_df[[stability_outcome_colname]], "_", my_grp, sep = "")
# check unique values in normalised data # check unique values in normalised data
cat("\nNo. of unique values in", stability_colname, "no rounding:" cat("\nNo. of unique values in", stability_colname, "no rounding:"
, length(unique(plotdf[[stability_colname]]))) , length(unique(plot_df[[stability_colname]])))
# Call the function to create the palette based on the group defined above # Call the function to create the palette based on the group defined above
#subcols_ps #subcols_ps
subcols_bp_hmap = ColourPalleteMulti(plotdf, stability_outcome_colname, stability_colname) subcols_bp_hmap = ColourPalleteMulti(plot_df, stability_outcome_colname, stability_colname)
cat("\nNo. of sub colours generated:", length(subcols_bp_hmap)) cat("\nNo. of sub colours generated:", length(subcols_bp_hmap))
@ -100,40 +100,54 @@ bp_stability_hmap <- function(plotdf = merged_df3
# Generate the subcols barplot # Generate the subcols barplot
#------------------------------- #-------------------------------
cowplot::plot_grid( cowplot::plot_grid(
ggplot(plotdf, aes_string(x = xvar_colname ggplot(plot_df, aes_string(x = xvar_colname
# , ordered = T) # , ordered = T)
)) + )) +
geom_bar(aes(fill = group) geom_bar(aes(fill = group)
, colour = "grey") + , colour = "grey") +
scale_fill_manual( values = subcols_bp_hmap scale_fill_manual( values = subcols_bp_hmap
, guide = "none") + , guide = "none") +
# scale_x_discrete("Position", labels=factor(plot_df$position)) +
theme( axis.text.x = element_text(size = my_xaxls theme(
, angle = 90 axis.text.x = element_text(size = my_xaxls
, hjust = 1 , angle = 90
, vjust = 0.4) , hjust = 1
, axis.text.y = element_text(size = my_yaxls , vjust = 0.4)
, angle = 0 , axis.text.y = element_text(size = my_yaxls
, hjust = 1 , angle = 0
, vjust = 0) , hjust = 1
, axis.title.x = element_text(size = my_xaxts) , vjust = 0)
, axis.title.y = element_text(size = my_yaxts ) , axis.title.x = element_blank()
, plot.title = element_text(size = my_pts #, axis.title.x = element_text(size = my_xaxts)
, hjust = 0.5)) + , axis.title.y = element_text(size = my_yaxts )
, plot.title = element_text(size = my_pts
, hjust = 0.5)) +
labs(title = p_title labs(title = p_title
, x = my_xlab , x = my_xlab
, y = my_ylab), , y = my_ylab),
geom_tile(aes(, tpos0 # heat-mapped distance tiles along the bot NULL,
, width = tW0 ggplot(plot_df,
, height = tH0) aes(x=factor(position), # THIS STUPID FUCKING FACTOR THING
, fill = plotdf$ligD_colours )
, colour = plotdf$ligD_colours ) +
, linetype = "blank"), #end of distance-heat-bar geom_tile(aes(y=0),
generate_distance_legend(plotdf), fill=plot_df$ligD_colours) +
ncol = 2, scale_x_discrete("Position", labels=factor(plot_df$position)) +
#align = "hv", theme_nothing() +
rel_widths = c(9/10, 0.4/10) theme(plot.background = element_rect(fill = "transparent", colour=NA),
plot.margin = margin(t=0,b=0)) +
labs(x = NULL, y = NULL), #end of distance-heat-bar
NULL,
position_annotation(plot_df),
#generate_distance_legend(plot_df),
ncol = 1,
align = "v",
rel_heights = c(10,-0.1,1,-0.1,1)
#rel_widths = c(9/10, 0.4/10)
) )
} }
bp_stability_hmap(small_df3)

87
scripts/functions/logoP_snp.R
View file

@ -250,64 +250,73 @@ LogoPlotSnps <- function(plot_df
, axis.title.y = element_text(size = y_tts , axis.title.y = element_text(size = y_tts
, colour = ytt_col) , colour = ytt_col)
, plot.background = element_rect(fill = theme_bgc) , plot.background = element_rect(fill = theme_bgc, colour=NA)
) ),
,ggseqlogo(tab_wt ggseqlogo(tab_wt
, method = 'custom' , method = 'custom'
, col_scheme = my_logo_col , col_scheme = my_logo_col
, seq_type = 'aa') + , seq_type = 'aa') +
scale_x_continuous(breaks = 1:ncol(tab_wt) scale_x_continuous(breaks = 1:ncol(tab_wt)
, expand = c(0.01,0) , expand = c(0.01,0)
, labels = colnames(tab_wt))+ , labels = as.factor(colnames(tab_wt))) +
theme(text = element_text(family="FreeSans") theme(text = element_text(family="FreeSans")
, legend.position = "none" , legend.position = "none"
, axis.text.x = element_blank() , axis.text.x = element_blank()
, axis.text.y = element_blank() , axis.text.y = element_blank()
, axis.title.x = element_blank() , axis.title.x = element_blank()
, axis.title.y = element_blank() , axis.title.y = element_blank()
, plot.background = element_rect(fill = theme_bgc) , plot.background = element_rect(fill = theme_bgc, colour=NA)
) + ) +
labs(x=NULL, y=NULL) labs(x=NULL, y=NULL),
, ggplot(
ggplot(data=unique_colour_map2, aes( data=unique_colour_map2,
x=factor(position), 0 # heat-mapped distance tiles along the bot aes(
, fill = position x=factor(position), 0 # heat-mapped distance tiles along the bot
, colour = position , fill = position
, linetype = "blank" , colour = position
) , linetype = "blank"
)
) + ) +
geom_tile() + geom_tile() +
theme(axis.text.x = element_text(size = x_ats theme(
, angle = x_tangle axis.text.x = element_blank()
, hjust = 1 , axis.ticks.x = element_blank()
, vjust = 0.4 # axis.text.x = element_text(size = x_ats
, colour = xfont_bgc) # , angle = x_tangle
, axis.text.y = element_blank() # , hjust = 1
, axis.ticks.y = element_blank() # , vjust = 0.4
, axis.title.x = element_text(size = x_tts # , colour = xfont_bgc)
, colour = xtt_col) , axis.text.y = element_blank()
, axis.title.y = element_text(size = y_tts , axis.ticks.y = element_blank()
, colour = ytt_col) , axis.title.x = element_blank()
, legend.title = element_text(size = leg_tts
, colour = ytt_col)
, legend.text = element_text(size = leg_ts)
, legend.position = leg_pos # , axis.title.x = element_text(size = x_tts
, legend.direction = leg_dir # , colour = xtt_col)
, plot.background = element_rect(fill = theme_bgc) # , axis.title.y = element_text(size = y_tts
, plot.margin = margin(t=0) # , colour = ytt_col)
, panel.grid=element_blank() # , legend.title = element_text(size = leg_tts
, panel.background = element_rect(fill = theme_bgc) # , colour = ytt_col)
, legend.text = element_text(size = leg_ts)
, legend.position = leg_pos
, legend.direction = leg_dir
, plot.background = element_rect(fill = theme_bgc, colour=NA)
, plot.margin = margin(t=0)
, panel.grid=element_blank()
, panel.background = element_rect(fill = theme_bgc, colour=NA)
) + ) +
scale_x_discrete(x_lab, labels=factor(unique_colour_map$position)) + scale_x_discrete(x_lab, labels=factor(unique_colour_map$position)) +
scale_color_manual(values=unique_colour_map$ligD_colours) + scale_color_manual(values=unique_colour_map$ligD_colours) +
scale_fill_manual(values=unique_colour_map$ligD_colours) + scale_fill_manual(values=unique_colour_map$ligD_colours) +
labs(y = NULL) labs(y = NULL)
, nrow = 3 , NULL
, position_annotation(plot_df, bg=theme_bgc)
, ncol=1
, align = "v" , align = "v"
, rel_heights = c(7/10, 2/7, 1/7)) , rel_heights = c(7/10, 2/7,1/7, -0.1, 0.5/7))
#------------------ #------------------
# Wild logo plot # Wild logo plot
#------------------ #------------------
} }
#LogoPlotSnps(mutable_df3)
#LogoPlotSnps(small_df3)

4
scripts/functions/wideP_consurf.R
View file

@ -27,7 +27,7 @@ wideP_consurf2 <- function(plot_df
, lower_EB_colname = "consurf_ci_lower" , lower_EB_colname = "consurf_ci_lower"
, plot_type = "point" # default is point , plot_type = "point" # default is point
, point_colours , point_colours = consurf_bp_colours
, p_size = 2 , p_size = 2
, leg_title1 = "" , leg_title1 = ""
, leg_labels = c("0": "Insufficient Data" , leg_labels = c("0": "Insufficient Data"
@ -321,7 +321,7 @@ wideP_consurf2 <- function(plot_df
g1_leg = g1_leg + geom_bar(aes_string(fill = sprintf("factor(%s)" g1_leg = g1_leg + geom_bar(aes_string(fill = sprintf("factor(%s)"
, yvar_colourN_colname))) , yvar_colourN_colname)))
g1_leg = g1_leg + scale_fill_manual(values = consurf_palette1 , name = leg_title1) g1_leg = g1_leg + scale_fill_manual(values = consurf_bp_colours , name = leg_title1)
g1_leg g1_leg
legend1 = get_legend(g1_leg) legend1 = get_legend(g1_leg)