111 lines
No EOL
4.7 KiB
R
111 lines
No EOL
4.7 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 SNP count: lineage lf data
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#########################################
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# Relevel factors so that x-axis categ appear as you want
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lin_lf_plot = lin_lf
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lin_lf_plot
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is.factor(lin_lf_plot$sel_lineages_f)
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lin_lf_plot$sel_lineages_f = factor(lin_lf_plot$sel_lineages_f, c(""
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, "L1"
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, "L2"
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, "L3"
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, "L4"
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, "L5"
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, "L6"
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, "L7"
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, "LBOV"
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, "L1;L2"
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, "L1;L3"
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, "L1;L4"
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, "L2;L3"
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, "L2;L3;L4"
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, "L2;L4"
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, "L2;L6"
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, "L2;LBOV"
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, "L3;L4"
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, "L4;L6"
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, "L4;L7"))
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levels(lin_lf_plot$sel_lineages_f)
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lin_count_bp(lin_lf_plot
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, x_categ = "sel_lineages_f"
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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_log10 = T
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, y_label = "Count"
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, y_scale_percent = F)
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###############################################
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# Lineage SNP diversity count: lineage wf data
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###############################################
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# Relevel factors so that x-axis categ appear as you want
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lin_wf_plot = lin_wf
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is.factor(lin_wf_plot$sel_lineages_f)
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lin_wf_plot$sel_lineages_f = factor(lin_wf_plot$sel_lineages_f, c(""
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, "L1"
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, "L2"
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, "L3"
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, "L4"
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, "L5"
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, "L6"
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, "L7"
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, "LBOV"
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, "L1;L2"
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, "L1;L3"
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, "L1;L4"
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, "L2;L3"
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, "L2;L3;L4"
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, "L2;L4"
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, "L2;L6"
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, "L2;LBOV"
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, "L3;L4"
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, "L4;L6"
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, "L4;L7"))
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levels(lin_wf_plot$sel_lineages_f)
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#==========
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# Plot
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#==========
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lin_count_bp(lin_wf_plot
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, x_categ = "sel_lineages_f"
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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 = "SNP diversity"
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)
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, x_categ = "sel_lineages_f"
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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 = 15
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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_log10 = T
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, y_scale_percent = F |