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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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22
scripts/plotting/plotting_thesis/thesis-figs-embb.R
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@ -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(