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bugfixes

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This commit is contained in:
Tanushree Tunstall 2023-02-27 20:02:10 +00:00
parent a405cd8035
commit 1c616eeb71
7 changed files with 77 additions and 51 deletions
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2
scripts/functions/bp_subcolours.R
View file

@ -47,7 +47,7 @@ bp_stability_hmap <- function(plot_df = merged_df3
my_yaxts = 10, # y-axis text size
my_pts = 10 # plot-title size
, my_xlab = "Position"
, my_ylab = "No. of SAVs"
, my_ylab = ""
# Custom 2: x-axis: geom tiles ~ lig distance
#, A_xvar_lig = T

11
scripts/functions/position_annotation.R
View file

@ -13,7 +13,8 @@ position_annotation=function(plot_df,
drug_colour='green',
lig1_colour='slategrey',
lig2_colour='navyblue',
lig3_colour='purple'
lig3_colour='purple',
x_label=NULL
)
{
x_ats = 12
@ -107,9 +108,9 @@ position_annotation=function(plot_df,
theme(plot.background = element_rect(fill = bg, colour=NA),
#plot.margin = margin(t=0,b=0),
panel.background = element_rect(fill = bg, colour=NA),
legend.position = "none"
legend.position = "none", axis.title.x = element_text(size = 8)
) +
labs(x = NULL, y= NULL) +
labs(x = x_label, y= NULL) +
geom_tile(aes(y = 1,x=reorder(position,-pos_count), fill = bg_all, colour = bg_all)
) +
geom_tile(aes(y = 2, x=reorder(position,-pos_count), fill = col_bg1, colour = col_bg1)
@ -146,9 +147,9 @@ position_annotation=function(plot_df,
theme(plot.background = element_rect(fill = bg, colour=NA),
#plot.margin = margin(t=0,b=0),
panel.background = element_rect(fill = bg, colour=NA),
legend.position = "none"
legend.position = "none", axis.title.x = element_text(size = 8)
) +
labs(x = NULL, y= NULL) +
labs(x = x_label, y= NULL) +
geom_tile(aes(y = 1, x=factor(position), fill = bg_all, colour = bg_all)
) +
geom_tile(aes(y = 2, x=factor(position), fill = col_bg1, colour = col_bg1)

21
scripts/plotting/plotting_thesis/thesis-figs-alr.R
View file

@ -166,7 +166,7 @@ print(paste0("Plotting LOW Rows: ", nrow(small_df3)))
logo_p_snps_low = LogoPlotSnps(
mutable_df3,
y_lab="",
y_lab="SAV Diversity",
aa_pos_drug=aa_pos_drug,
active_aa_pos=active_aa_pos,
aa_pos_lig1=aa_pos_lig1,
@ -195,7 +195,7 @@ logo_or_low = LogoPlotCustomH(
lig3_colour = tile_map$tile_colour[4]
)
stability_low = stab()+ annotate(geom="text", label="Position",x=0.5,y=0.025, size=3)
stability_low = stab()+ annotate(geom="text", label="Wild-Type Position",x=0.5,y=0.025, size=3)
# MID
@ -205,7 +205,7 @@ print(paste0("Plotting MID Rows: ", nrow(small_df3)))
logo_p_snps_centre = LogoPlotSnps(
mutable_df3,
y_lab = "",
y_lab = "SAV Diversity",
aa_pos_drug=aa_pos_drug,
active_aa_pos=active_aa_pos,
aa_pos_lig1=aa_pos_lig1,
@ -231,7 +231,7 @@ logo_or_centre = LogoPlotCustomH(
lig3_colour = tile_map$tile_colour[4]
)
stability_centre = stab(my_ylab="SAV Count")
stability_centre = stab()
# HIGH
small_df3 = merged_df3[merged_df3['position'] > centre,]
@ -241,7 +241,7 @@ print(paste0("Plotting HIGH Rows: ", nrow(small_df3)))
logo_p_snps_high = LogoPlotSnps(
mutable_df3,
y_lab="" ,
y_lab="SAV Diversity" ,
aa_pos_drug=aa_pos_drug,
active_aa_pos=active_aa_pos,
aa_pos_lig1=aa_pos_lig1,
@ -251,7 +251,7 @@ logo_p_snps_high = LogoPlotSnps(
lig1_colour = tile_map$tile_colour[2],
lig2_colour = tile_map$tile_colour[3],
lig3_colour = tile_map$tile_colour[4]
)+ annotate(geom="text", label="Position",x=0.5,y=0.025, size=3)
)+ annotate(geom="text", label="Wild-Type Position",x=0.5,y=0.025, size=3)
logo_or_high = LogoPlotCustomH(
small_df3,
@ -267,10 +267,10 @@ logo_or_high = LogoPlotCustomH(
lig1_colour = tile_map$tile_colour[2],
lig2_colour = tile_map$tile_colour[3],
lig3_colour = tile_map$tile_colour[4]
)+ annotate(geom="text", label="Position",x=0.5,y=0.025, size=3)
)+ annotate(geom="text", label="Wild-Type Position",x=0.5,y=0.025, size=3)
stability_high = stab()+ annotate(geom="text", label="Position",x=0.5,y=0.025, size=3)
stability_high = stab()+ annotate(geom="text", label="Wild-Type Position",x=0.5,y=0.025, size=3)
#### "sorted" stability plots ####
# do stability plots for later assembly
@ -292,9 +292,10 @@ stability_high_reorder = bp_stability_hmap(
drug_colour = tile_map$tile_colour[1],
lig1_colour = tile_map$tile_colour[2],
lig2_colour = tile_map$tile_colour[3],
lig3_colour = tile_map$tile_colour[4]
lig3_colour = tile_map$tile_colour[4],
x_label="Wild-Type Position"
)+ annotate(geom="text", label="Position",x=0.5,y=0.025, size=3)
)
stability_centre_reorder = bp_stability_hmap(
snpcount_low_high_df,
reorder_position = T,

22
scripts/plotting/plotting_thesis/thesis-figs-embb.R
View file

@ -12,6 +12,7 @@ source("~/git/LSHTM_analysis/scripts/plotting/get_plotting_dfs.R")
#outdir="/home/pub/Work/LSHTM/Thesis_Plots/"
outdir="~/git/Writing/thesis/tex/images-corrected/embb/"
#outdir="~/tmp/embb/"
# add "pos_count" position count column
merged_df3=merged_df3 %>% dplyr::add_count(position)
@ -83,8 +84,9 @@ stability_low = bp_stability_hmap(snpcount_low_low_df,
active_aa_pos=active_aa_pos,
aa_pos_lig1=aa_pos_lig1,
aa_pos_lig2=aa_pos_lig2,
aa_pos_lig3=aa_pos_lig3
)+ annotate(geom="text", label="Position",x=0.5,y=0.025, size=3)
aa_pos_lig3=aa_pos_lig3,
x_label="Wild-Type Position"
)
low=round(max(merged_df3$position)/3)
centre=low*2
@ -175,7 +177,7 @@ print(paste0("Plotting LOW Rows: ", nrow(small_df3)))
logo_p_snps_low = LogoPlotSnps(mutable_df3,
y_lab="",
y_lab="SAV Diversity",
aa_pos_drug=aa_pos_drug,
active_aa_pos=active_aa_pos,
aa_pos_lig1=aa_pos_lig1,
@ -207,13 +209,13 @@ logo_p_snps_centre = LogoPlotSnps(
aa_pos_lig1=aa_pos_lig1,
aa_pos_lig2=aa_pos_lig2,
aa_pos_lig3=aa_pos_lig3,
y_lab = "SAV Count"
y_lab = "SAV Diversity"
)
logo_or_centre = LogoPlotCustomH(small_df3,
y_axis_increment=2,
y_lab = "Log(10) Odds Ratio",
y_axis_log = TRUE,
y_axis_increment=10,
y_lab = "Odds Ratio",
y_axis_log = FALSE,
rm_empty_y=T,
aa_pos_drug=aa_pos_drug,
active_aa_pos=active_aa_pos,
@ -229,14 +231,14 @@ print(paste0("Plotting HIGH Rows: ", nrow(small_df3)))
logo_p_snps_high = LogoPlotSnps(mutable_df3,
y_lab="",
y_lab="SAV Diversity",
x_lab = "Position",
aa_pos_drug=aa_pos_drug,
active_aa_pos=active_aa_pos,
aa_pos_lig1=aa_pos_lig1,
aa_pos_lig2=aa_pos_lig2,
aa_pos_lig3=aa_pos_lig3
) + annotate(geom="text", label="Position",x=0.5,y=0.025, size=3)
) + annotate(geom="text", label="Wild-Type Position",x=0.5,y=0.025, size=3)
logo_or_high = LogoPlotCustomH(small_df3,
@ -248,7 +250,7 @@ logo_or_high = LogoPlotCustomH(small_df3,
aa_pos_lig1=aa_pos_lig1,
aa_pos_lig2=aa_pos_lig2,
aa_pos_lig3=aa_pos_lig3
)+ annotate(geom="text", label="Position",x=0.5,y=0.025, size=3)
)+ annotate(geom="text", label="Wild-Type Position",x=0.5,y=0.025, size=3)
jpeg(paste0(outdir,"embb_average_stability.jpeg"), height = 8.25, width=11.5, unit="in",res=300)
cowplot::plot_grid(

35
scripts/plotting/plotting_thesis/thesis-figs-gid.R
View file

@ -136,7 +136,7 @@ stab=function(...){bp_stability_hmap(
yvar_colname = 'avg_stability_scaled',
stability_colname = "avg_stability_scaled",
stability_outcome_colname = "avg_stability_outcome",
my_ylab = "",
#my_ylab = "",
my_xaxls = 6, # x-axis label size
my_yaxls = 8, # y-axis label size
drug_colour = tile_map$tile_colour[1],
@ -163,7 +163,7 @@ print(paste0("Plotting LOW Rows: ", nrow(small_df3)))
logo_p_snps_low = LogoPlotSnps(
mutable_df3,
y_lab="",
y_lab="SAV Diversity",
aa_pos_drug=aa_pos_drug,
active_aa_pos=active_aa_pos,
aa_pos_lig1=aa_pos_lig1,
@ -203,7 +203,7 @@ mutable_df3 = cbind(small_df3)
print(paste0("Plotting MID Rows: ", nrow(small_df3)))
logo_p_snps_centre = LogoPlotSnps(
mutable_df3,
y_lab = "",
y_lab = "SAV Diversity",
aa_pos_drug=aa_pos_drug,
active_aa_pos=active_aa_pos,
aa_pos_lig1=aa_pos_lig1,
@ -229,7 +229,26 @@ logo_or_centre = LogoPlotCustomH(
lig3_colour = tile_map$tile_colour[4]
)
stability_centre = stab()
stability_centre = bp_stability_hmap(
small_df3,
p_title = NULL,
yvar_colname = 'avg_stability_scaled',
stability_colname = "avg_stability_scaled",
stability_outcome_colname = "avg_stability_outcome",
my_ylab = "SAV Count",
my_xaxls = 6, # x-axis label size
my_yaxls = 8, # y-axis label size
drug_colour = tile_map$tile_colour[1],
lig1_colour = tile_map$tile_colour[2],
lig2_colour = tile_map$tile_colour[3],
lig3_colour = tile_map$tile_colour[4],
y_max_override=max(merged_df3$pos_count),
aa_pos_drug=aa_pos_drug,
active_aa_pos=active_aa_pos,
aa_pos_lig1=aa_pos_lig1,
aa_pos_lig2=aa_pos_lig2,
aa_pos_lig3=aa_pos_lig3
)
# HIGH
small_df3 = merged_df3[merged_df3['position'] > centre,]
@ -239,7 +258,7 @@ print(paste0("Plotting HIGH Rows: ", nrow(small_df3)))
logo_p_snps_high = LogoPlotSnps(
mutable_df3,
y_lab="" ,
y_lab="SAV Diversity" ,
aa_pos_drug=aa_pos_drug,
active_aa_pos=active_aa_pos,
aa_pos_lig1=aa_pos_lig1,
@ -249,7 +268,7 @@ logo_p_snps_high = LogoPlotSnps(
lig1_colour = tile_map$tile_colour[2],
lig2_colour = tile_map$tile_colour[3],
lig3_colour = tile_map$tile_colour[4]
)+ annotate(geom="text", label="Position",x=0.5,y=0.025, size=3)
)+ annotate(geom="text", label="Wild-Type Position",x=0.5,y=0.025, size=3)
logo_or_high = LogoPlotCustomH(
small_df3,
@ -265,10 +284,10 @@ logo_or_high = LogoPlotCustomH(
lig1_colour = tile_map$tile_colour[2],
lig2_colour = tile_map$tile_colour[3],
lig3_colour = tile_map$tile_colour[4]
)+ annotate(geom="text", label="Position",x=0.5,y=0.025, size=3)
)+ annotate(geom="text", label="Wild-Type Position",x=0.5,y=0.025, size=3)
stability_high = stab()+ annotate(geom="text", label="Position",x=0.5,y=0.025, size=3)
stability_high = stab(x_label="Wild-Type Position")
#### "sorted" stability plots ####
# do stability plots for later assembly

17
scripts/plotting/plotting_thesis/thesis-figs-katg.R
View file

@ -165,7 +165,7 @@ print(paste0("Plotting LOW Rows: ", nrow(small_df3)))
logo_p_snps_low = LogoPlotSnps(
mutable_df3,
y_lab="",
y_lab="SAV Diversity",
aa_pos_drug=aa_pos_drug,
active_aa_pos=active_aa_pos,
aa_pos_lig1=aa_pos_lig1,
@ -195,7 +195,7 @@ logo_or_low = LogoPlotCustomH(
lig3_colour = tile_map$tile_colour[4]
)
stability_low = stab()+ annotate(geom="text", label="Position",x=0.5,y=0.025, size=3)
stability_low = stab(x_label="Wild-Type Position")
# MID
@ -205,7 +205,7 @@ print(paste0("Plotting MID Rows: ", nrow(small_df3)))
logo_p_snps_centre = LogoPlotSnps(
mutable_df3,
y_lab = "",
y_lab = "SAV Diversity",
aa_pos_drug=aa_pos_drug,
active_aa_pos=active_aa_pos,
aa_pos_lig1=aa_pos_lig1,
@ -244,7 +244,7 @@ print(paste0("Plotting HIGH Rows: ", nrow(small_df3)))
logo_p_snps_high = LogoPlotSnps(
mutable_df3,
y_lab="" ,
y_lab="SAV Diversity" ,
aa_pos_drug=aa_pos_drug,
active_aa_pos=active_aa_pos,
aa_pos_lig1=aa_pos_lig1,
@ -254,7 +254,7 @@ logo_p_snps_high = LogoPlotSnps(
lig1_colour = tile_map$tile_colour[2],
lig2_colour = tile_map$tile_colour[3],
lig3_colour = tile_map$tile_colour[4]
)+ annotate(geom="text", label="Position",x=0.5,y=0.025, size=3)
)+ annotate(geom="text", label="Wild-Type Position",x=0.5,y=0.025, size=3)
logo_or_high = LogoPlotCustomH(
small_df3,
@ -271,7 +271,7 @@ logo_or_high = LogoPlotCustomH(
lig1_colour = tile_map$tile_colour[2],
lig2_colour = tile_map$tile_colour[3],
lig3_colour = tile_map$tile_colour[4]
)+ annotate(geom="text", label="Position",x=0.5,y=0.025, size=3)
)+ annotate(geom="text", label="Wild-Type Position",x=0.5,y=0.025, size=3)
stability_high = stab()
@ -298,7 +298,7 @@ stability_high_reorder = bp_stability_hmap(
lig2_colour = tile_map$tile_colour[3],
lig3_colour = tile_map$tile_colour[4]
)+ annotate(geom="text", label="Position",x=0.5,y=0.025, size=3)
)+ annotate(geom="text", label="Wild-Type Position",x=0.5,y=0.025, size=3)
stability_centre_reorder = bp_stability_hmap(
snpcount_low_high_df,
reorder_position = T,
@ -340,7 +340,8 @@ stability_low_reorder = bp_stability_hmap(
drug_colour = tile_map$tile_colour[1],
lig1_colour = tile_map$tile_colour[2],
lig2_colour = tile_map$tile_colour[3],
lig3_colour = tile_map$tile_colour[4]
lig3_colour = tile_map$tile_colour[4],
x_label="Wild-Type Position"
)

18
scripts/plotting/plotting_thesis/thesis-figs-rpob.R
View file

@ -164,7 +164,7 @@ print(paste0("Plotting LOW Rows: ", nrow(small_df3)))
logo_p_snps_low = LogoPlotSnps(
mutable_df3,
y_lab="",
y_lab="SAV Diversity",
active_aa_pos=active_aa_pos,
aa_pos_drug=aa_pos_drug,
aa_pos_lig1=aa_pos_lig1,
@ -204,7 +204,7 @@ print(paste0("Plotting MID Rows: ", nrow(small_df3)))
logo_p_snps_centre = LogoPlotSnps(
mutable_df3,
y_lab = "",
y_lab = "SAV Diversity",
x_ats = 4.5,
active_aa_pos=active_aa_pos,
aa_pos_drug=aa_pos_drug,
@ -246,7 +246,7 @@ print(paste0("Plotting HIGH Rows: ", nrow(small_df3)))
logo_p_snps_high = LogoPlotSnps(
mutable_df3,
y_lab=" " ,
y_lab="SAV Diversity" ,
x_ats = 5,
active_aa_pos=active_aa_pos,
aa_pos_drug=aa_pos_drug,
@ -257,7 +257,7 @@ logo_p_snps_high = LogoPlotSnps(
lig1_colour = tile_map$tile_colour[2],
lig2_colour = tile_map$tile_colour[3],
lig3_colour = tile_map$tile_colour[4]
)+ annotate(geom="text", label="Position",x=0.5,y=0.025, size=3)
)+ annotate(geom="text", label="Wild-Type Position",x=0.5,y=0.025, size=3)
logo_or_high = LogoPlotCustomH(
small_df3,
@ -274,10 +274,11 @@ logo_or_high = LogoPlotCustomH(
lig1_colour = tile_map$tile_colour[2],
lig2_colour = tile_map$tile_colour[3],
lig3_colour = tile_map$tile_colour[4]
)+ annotate(geom="text", label="Position",x=0.5,y=0.025, size=3)
)+ annotate(geom="text", label="Wild-Type Position",x=0.5,y=0.025, size=3)
stability_low = stab(my_xaxls = 4)+ annotate(geom="text", label="Position",x=0.5,y=0.025, size=3)
stability_low = stab(my_xaxls = 4,
x_label="Wild-Type Position")
#### "sorted" stability plots ####
# do stability plots for later assembly
@ -301,7 +302,7 @@ stability_high_reorder = bp_stability_hmap(
lig2_colour = tile_map$tile_colour[3],
lig3_colour = tile_map$tile_colour[4]
)+ annotate(geom="text", label="Position",x=0.5,y=0.025, size=3)
)+ annotate(geom="text", label="Wild-Type Position",x=0.5,y=0.025, size=3)
stability_centre_reorder = bp_stability_hmap(
snpcount_low_high_df,
reorder_position = T,
@ -343,7 +344,8 @@ stability_low_reorder = bp_stability_hmap(
drug_colour = tile_map$tile_colour[1],
lig1_colour = tile_map$tile_colour[2],
lig2_colour = tile_map$tile_colour[3],
lig3_colour = tile_map$tile_colour[4]
lig3_colour = tile_map$tile_colour[4],
x_label="Wild-Type Position"
)