62 lines
2.1 KiB
R
62 lines
2.1 KiB
R
setwd("~/git/LSHTM_analysis/scripts/plotting")
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source ('get_plotting_dfs.R')
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source("../functions/bp_lineage.R")
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#########################################
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# Lineage and SAV count: lineage lf data
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#########################################
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#=========================
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# Data: All lineages or
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# selected few
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#=========================
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sel_lineages = levels(lin_lf$sel_lineages_f)
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sel_lineages
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lin_lf_plot = lin_lf[lin_lf$sel_lineages_f%in%sel_lineages,]
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# drop unused factor levels
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lin_lf_plot$sel_lineages_f = factor(lin_lf_plot$sel_lineages_f)
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levels(lin_lf_plot$sel_lineages_f)
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#=========================
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# Lineage count plot
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#=========================
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lin_count_bp(lin_lf_plot = lin_lf
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, x_categ = "sel_lineages"
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, y_count = "p_count"
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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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, x_lab_angle = 90
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, my_xats = 20
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, bar_col_labels = c("Mutations", "Total Samples")
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, bar_col_values = c("grey50", "gray75")
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, y_scale_percent = F # T for diversity
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, y_log10 = F
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, y_label = "Count")
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###############################################
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# Lineage SAV diversity count: lineage wf data
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###############################################
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#=========================
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# Data: All lineages or
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# selected few
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#=========================
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sel_lineages = levels(lin_wf$sel_lineages_f)
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sel_lineages
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lin_wf_plot = lin_wf[lin_wf$sel_lineages_f%in%sel_lineages,]
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# drop unused factor levels
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lin_wf_plot$sel_lineages_f = factor(lin_wf_plot$sel_lineages_f)
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levels(lin_wf_plot$sel_lineages_f)
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#=========================
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# Lineage Diversity plot
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#=========================
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lin_count_bp(lin_wf_plot = lin_wf
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, x_categ = "sel_lineages"
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, y_count = "snp_diversity"
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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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, my_xats = 20
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, y_scale_percent = T
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, y_label = "SAV diversity")
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