tanu/LSHTM_analysis
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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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21
scripts/plotting/plotting_thesis/thesis-figs-alr.R
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@ -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,