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Tanushree Tunstall 2022-08-27 15:35:41 +01:00
parent 79b251047d
commit c6f5a446c3
6 changed files with 56 additions and 55 deletions
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6
scripts/functions/bp_subcolours.R
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@ -56,7 +56,8 @@ bp_stability_hmap <- function(plot_df = merged_df3
, tW0 = 1 , tW0 = 1
, tH0 = 0.2, , tH0 = 0.2,
y_max_override = 1, # an override for tidily plotting multiple different-ranged plots together y_max_override = 1, # an override for tidily plotting multiple different-ranged plots together
reorder_position = FALSE # enable to reorder according to plot_df$pos_count reorder_position = FALSE, # enable to reorder according to plot_df$pos_count
...
@ -103,7 +104,8 @@ bp_stability_hmap <- function(plot_df = merged_df3
active_aa_pos=active_aa_pos, active_aa_pos=active_aa_pos,
aa_pos_lig1=aa_pos_lig1, aa_pos_lig1=aa_pos_lig1,
aa_pos_lig2=aa_pos_lig2, aa_pos_lig2=aa_pos_lig2,
aa_pos_lig3=aa_pos_lig3 aa_pos_lig3=aa_pos_lig3,
...
) )
subcols_plot = ggplot(plot_df) + subcols_plot = ggplot(plot_df) +

22
scripts/functions/logoP_or.R
View file

@ -61,25 +61,12 @@ LogoPlotCustomH <- function(plot_df
, leg_tts = 8 # leg title size , leg_tts = 8 # leg title size
, tpos0 = 0 # 0 is a magic number that does my sensible default , tpos0 = 0 # 0 is a magic number that does my sensible default
, tW0 = 1 , tW0 = 1
, tH0 = 0.3 , tH0 = 0.3,
...
) )
{ {
#################################
# Data processing for logo plot
#################################
# plot_df = generate_distance_colour_map(plot_df, debug=TRUE)
# unique_colour_map = unique(plot_df[,c("position","ligD_colours")])
# unique_colour_map = unique_colour_map[order(unique_colour_map$position), ]
# rownames(unique_colour_map) = unique_colour_map$position
#
# unique_colour_map2 = unique_colour_map
# unique_colour_map2$position=as.factor(unique_colour_map2$position)
# unique_colour_map2$ligD_colours = as.factor(unique_colour_map2$ligD_colours)
#
if (rm_empty_y){ if (rm_empty_y){
cat(paste0("Original Rows: ",nrow(plot_df))) cat(paste0("Original Rows: ",nrow(plot_df)))
plot_df = plot_df[!is.na(plot_df[y_axis_colname]),] plot_df = plot_df[!is.na(plot_df[y_axis_colname]),]
@ -231,7 +218,8 @@ LogoPlotCustomH <- function(plot_df
active_aa_pos=active_aa_pos, active_aa_pos=active_aa_pos,
aa_pos_lig1=aa_pos_lig1, aa_pos_lig1=aa_pos_lig1,
aa_pos_lig2=aa_pos_lig2, aa_pos_lig2=aa_pos_lig2,
aa_pos_lig3=aa_pos_lig3 aa_pos_lig3=aa_pos_lig3,
...
), ),
ncol=1, align='v', rel_heights = c(6,1) ncol=1, align='v', rel_heights = c(6,1)

6
scripts/functions/logoP_snp.R
View file

@ -51,7 +51,8 @@ LogoPlotSnps <- function(plot_df
, tpos0 = 0 # 0 is a magic number that does my sensible default , tpos0 = 0 # 0 is a magic number that does my sensible default
, tW0 = 1 , tW0 = 1
, tH0 = 0.2 , tH0 = 0.2
, debug=FALSE , debug=FALSE,
...
) )
@ -286,7 +287,8 @@ LogoPlotSnps <- function(plot_df
active_aa_pos=active_aa_pos, active_aa_pos=active_aa_pos,
aa_pos_lig1=aa_pos_lig1, aa_pos_lig1=aa_pos_lig1,
aa_pos_lig2=aa_pos_lig2, aa_pos_lig2=aa_pos_lig2,
aa_pos_lig3=aa_pos_lig3) aa_pos_lig3=aa_pos_lig3,
...)
#aligned=align_plots(logo_top, logo_bottom, anno_bar, align='vh', axis='lr') #aligned=align_plots(logo_top, logo_bottom, anno_bar, align='vh', axis='lr')
cowplot::plot_grid( cowplot::plot_grid(

8
scripts/functions/position_annotation.R
View file

@ -186,5 +186,9 @@ position_annotation=function(plot_df,
# active_aa_pos=1:1000, # active_aa_pos=1:1000,
# aa_pos_lig1=1:1000, # aa_pos_lig1=1:1000,
# aa_pos_lig2=1:1000, # aa_pos_lig2=1:1000,
# aa_pos_lig3=1:1000 # aa_pos_lig3=1:1000,
# ) # drug_colour = "red",
# lig1_colour = "green",
# lig2_colour = "blue",
# lig3_colour = "skyblue"
# )

26
scripts/functions/position_count_bp.R
View file

@ -22,20 +22,22 @@ theme_set(theme_grey())
# visually might be nicer for it to be inside the plot # visually might be nicer for it to be inside the plot
#================================================================= #=================================================================
site_snp_count_bp <- function (plotdf site_snp_count_bp <- function (plotdf,
, df_colname = "position" df_colname = "position",
#, bp_plot_title = "" #, bp_plot_title = ""
#, leg_title = "Legend title" #, leg_title = "Legend title"
, leg_text_size = 10#20 leg_text_size = 10,#20
, axis_text_size = 10#25 axis_text_size = 10,#25
, axis_label_size = 10#22 axis_label_size = 10,#22
, subtitle_size = 10#20 subtitle_size = 10,#20
, geom_ls = 10 geom_ls = 10,
, xaxis_title = "Number of nsSNPs" xaxis_title = "Number of nsSNPs",
, yaxis_title = "Number of Sites" yaxis_title = "Number of Sites",
, title_colour = "chocolate4" title_colour = "chocolate4",
, subtitle_text = NULL subtitle_text = NULL,
, subtitle_colour = "pink") subtitle_colour = "pink",
...
)
{ {
plotdf = as.data.frame(plotdf) plotdf = as.data.frame(plotdf)

43
scripts/plotting/plotting_thesis/alr/gg_pairs_all_alr.R
View file

@ -5,7 +5,7 @@
#======= #=======
# output # output
#======= #=======
#outdir_images = paste0("~/git/Writing/thesis/images/results/", tolower(gene), "/") outdir_images = paste0("/home/pub/Work/LSHTM/Thesis_Plots/pairs/")
#cat("plots will output to:", outdir_images) #cat("plots will output to:", outdir_images)
my_gg_pairs=function(plot_df, plot_title my_gg_pairs=function(plot_df, plot_title
@ -20,28 +20,31 @@ my_gg_pairs=function(plot_df, plot_title
title="ρ", title="ρ",
digits=2, digits=2,
justify_labels = "centre", justify_labels = "centre",
title_args=list(size=tt_args_size, colour="black"),#2.5 title_args=list(size=tt_args_size, colour="black")#,#2.5
group_args=list(size=gp_args_size)#2.5 #group_args=list(size=gp_args_size)#2.5
) )
), ),
lower = list( lower = list(
continuous = wrap("points", continuous = wrap(
alpha = 0.7, "points",
size=0.125), alpha = 0.7,
combo = wrap("dot", size=0.125
alpha = 0.7,
size=0.125)
), ),
aes(colour = factor(ifelse(dst_mode==0, combo = wrap(
"S", "dot",
"R") ), alpha = 0.7,
alpha = 0.5), size=0.125)
title=plot_title) + ),
# aes(colour = factor(ifelse(dst_mode==0,
scale_colour_manual(values = c("red", "blue")) + # "S",
scale_fill_manual(values = c("red", "blue")) #+ # "R") ),
# theme(text = element_text(size=7, # alpha = 0.5),
# face="bold")) title=plot_title) #+
#
# scale_colour_manual(values = c("red", "blue")) +
# scale_fill_manual(values = c("red", "blue")) #+
# theme(text = element_text(size=7,
# face="bold"))
} }
DistCutOff = 10 DistCutOff = 10
@ -152,7 +155,7 @@ plot_corr_df_aff = my_gg_pairs(corr_df_aff
, plot_title="Affinity estimates" , plot_title="Affinity estimates"
#, tt_args_size = 4 #, tt_args_size = 4
#, gp_args_size = 4 #, gp_args_size = 4
) )
#### Combine plots ##### #### Combine plots #####
# #png("/home/tanu/tmp/gg_pairs_all.png", height = 6, width=11.75, unit="in",res=300) # #png("/home/tanu/tmp/gg_pairs_all.png", height = 6, width=11.75, unit="in",res=300)