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SNP -> SAV for thesis plots

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This commit is contained in:
Tanushree Tunstall 2023-02-19 17:43:22 +00:00
parent 777d3765cf
commit db7e2912e1
31 changed files with 145 additions and 145 deletions
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10
scripts/plotting/plotting_thesis/pnca/lineage_bp_dist.R
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@ -41,7 +41,7 @@ my_yals = 8 # y axis label size
my_lls = 8 # legend label size
d_lab_size = 2.3
#===============================
# lineage sample and SNP count
# lineage sample and SAV count
#===============================
lin_countP = lin_count_bp(lf_data = lineage_dfL[['lin_lf']]
, all_lineages = F
@ -58,7 +58,7 @@ lin_countP = lin_count_bp(lf_data = lineage_dfL[['lin_lf']]
, my_xals = my_xals # x axis label size
, my_yals = my_yals # y axis label size
, my_lls = my_lls # legend label size
, bar_col_labels = c("nsSNPs", "Total Samples")
, bar_col_labels = c("SAVs", "Total Samples")
, bar_col_values = c("grey50", "gray75")
, bar_leg_name = ""
, leg_location = "top"
@ -68,7 +68,7 @@ lin_countP = lin_count_bp(lf_data = lineage_dfL[['lin_lf']]
)
lin_countP
#===============================
# lineage SNP diversity count
# lineage SAV diversity count
#===============================
lin_diversityP = lin_count_bp_diversity(lf_data = lineage_dfL[['lin_wf']]
, x_categ = "sel_lineages"
@ -87,8 +87,8 @@ lin_diversityP = lin_count_bp_diversity(lf_data = lineage_dfL[['lin_wf']]
, y_log10 = F
, y_scale_percent = F
, leg_location = "top"
, y_label = "Percent" #"SNP diversity"
, bp_plot_title = "nsSNP diversity"
, y_label = "Percent" #"SAV diversity"
, bp_plot_title = "SAV diversity"
, title_colour = "black" #"chocolate4"
, subtitle_text = NULL
, sts = 10