SNP -> SAV for thesis plots
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777d3765cf
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31 changed files with 145 additions and 145 deletions
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@ -41,7 +41,7 @@ my_yals = 8 # y axis label size
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my_lls = 8 # legend label size
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d_lab_size = 2.3
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#===============================
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# lineage sample and SNP count
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# lineage sample and SAV count
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#===============================
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lin_countP = lin_count_bp(lf_data = lineage_dfL[['lin_lf']]
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, all_lineages = F
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@ -58,7 +58,7 @@ lin_countP = lin_count_bp(lf_data = lineage_dfL[['lin_lf']]
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, my_xals = my_xals # x axis label size
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, my_yals = my_yals # y axis label size
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, my_lls = my_lls # legend label size
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, bar_col_labels = c("nsSNPs", "Total Samples")
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, bar_col_labels = c("SAVs", "Total Samples")
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, bar_col_values = c("grey50", "gray75")
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, bar_leg_name = ""
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, leg_location = "top"
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@ -68,7 +68,7 @@ lin_countP = lin_count_bp(lf_data = lineage_dfL[['lin_lf']]
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)
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lin_countP
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#===============================
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# lineage SNP diversity count
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# lineage SAV diversity count
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#===============================
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lin_diversityP = lin_count_bp_diversity(lf_data = lineage_dfL[['lin_wf']]
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, x_categ = "sel_lineages"
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@ -87,8 +87,8 @@ lin_diversityP = lin_count_bp_diversity(lf_data = lineage_dfL[['lin_wf']]
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, y_log10 = F
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, y_scale_percent = F
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, leg_location = "top"
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, y_label = "Percent" #"SNP diversity"
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, bp_plot_title = "nsSNP diversity"
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, y_label = "Percent" #"SAV diversity"
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, bp_plot_title = "SAV diversity"
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, title_colour = "black" #"chocolate4"
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, subtitle_text = NULL
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, sts = 10
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