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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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35
scripts/plotting/plotting_thesis/thesis-figs-gid.R
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@ -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