68 lines
No EOL
2.9 KiB
R
68 lines
No EOL
2.9 KiB
R
# get plotting_dfs()
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# using dfs [lf and wf] from lineage_dfL
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#===============================
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# lineage sample and SNP 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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, x_categ = "sel_lineages"
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, y_count = "p_count"
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, use_lineages = c("L1", "L2", "L3", "L4")
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, bar_fill_categ = "count_categ"
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, display_label_col = "p_count"
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, bar_stat_stype = "identity"
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, d_lab_size = 10
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, d_lab_col = "black"
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, my_xats = 25 # x axis text size
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, my_yats = 25 # y axis text size
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, my_xals = 25 # x axis label size
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, my_yals = 25 # y axis label size
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, my_lls = 25 # legend label size
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, bar_col_labels = c("SNPs", "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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, y_log10 = F
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, y_scale_percent = FALSE
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, y_label = c("Count")
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)
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#===============================
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# lineage SNP 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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, y_count = "snp_diversity"
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#, all_lineages = F
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, use_lineages = c("L1", "L2", "L3", "L4")
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, display_label_col = "snp_diversity_f"
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, bar_stat_stype = "identity"
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, x_lab_angle = 90
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, d_lab_size =10
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, my_xats = 25 # x axis text size
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, my_yats = 25 # y axis text size
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, my_xals = 25 # x axis label size
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, my_yals = 25 # y axis label size
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, my_lls = 25 # legend label size
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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 = "SNP diversity")
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#=============================================
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# Output plots: Lineage count and Diversity
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#=============================================
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lineage_bp_CL = paste0(outdir_images
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,tolower(gene)
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,"_lineage_bp_CL.svg")
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cat("Lineage barplots:", lineage_bp_CL)
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svg(lineage_bp_CL, width = 8, height = 15)
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cowplot::plot_grid(lin_countP, lin_diversityP
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#, labels = c("(a)", "(b)", "(c)", "(d)")
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, nrow = 2
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, labels = "AUTO"
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, label_size = 25)
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dev.off() |