added linage barplots

scripts/plotting/plotting_thesis/lineage_barplots_combined.R

@@ -0,0 +1,68 @@
+# get plotting_dfs()
+# using dfs [lf and wf] from lineage_dfL
+#===============================
+# lineage sample and SNP count
+#===============================
+lin_countP = lin_count_bp(lf_data = lineage_dfL[['lin_lf']]
+             , all_lineages = F
+             , x_categ = "sel_lineages"
+             , y_count = "p_count"
+             , use_lineages = c("L1", "L2", "L3", "L4")
+             , bar_fill_categ = "count_categ"
+             , display_label_col = "p_count"
+             , bar_stat_stype = "identity"
+             , d_lab_size = 10
+             , d_lab_col = "black"
+             , my_xats = 25 # x axis text size
+             , my_yats = 25 # y axis text size
+             , my_xals = 25 # x axis label size
+             , my_yals = 25 # y axis label size
+             , my_lls  = 25 # legend label size
+             , bar_col_labels =  c("SNPs", "Total Samples")
+             , bar_col_values = c("grey50", "gray75")
+             , bar_leg_name = ""
+             , leg_location = "top"
+             , y_log10 = F
+             , y_scale_percent = FALSE
+             , y_label = c("Count")
+             )
+
+#===============================
+# lineage SNP diversity count
+#===============================
+lin_diversityP = lin_count_bp_diversity(lf_data = lineage_dfL[['lin_wf']]
+                              , x_categ = "sel_lineages"
+                              , y_count = "snp_diversity"
+                              #, all_lineages = F
+                              , use_lineages = c("L1", "L2", "L3", "L4")
+                              , display_label_col = "snp_diversity_f"
+                              , bar_stat_stype = "identity"
+                              , x_lab_angle = 90
+                              , d_lab_size =10
+                              , my_xats = 25 # x axis text size
+                              , my_yats = 25 # y axis text size
+                              , my_xals = 25 # x axis label size
+                              , my_yals = 25 # y axis label size
+                              , my_lls  = 25 # legend label size
+                              , y_log10 = F
+                              , y_scale_percent = F
+                              , leg_location = "top"
+                              , y_label = "SNP diversity")
+
+#=============================================
+# Output plots: Lineage count and Diversity
+#=============================================
+lineage_bp_CL =  paste0(outdir_images
+                        ,tolower(gene)
+                        ,"_lineage_bp_CL.svg")
+
+cat("Lineage barplots:", lineage_bp_CL)
+svg(lineage_bp_CL, width = 8, height = 15)
+
+cowplot::plot_grid(lin_countP, lin_diversityP
+                                         #, labels = c("(a)", "(b)", "(c)", "(d)")
+                                         , nrow = 2
+                                         , labels = "AUTO"
+                                         , label_size = 25)
+
+dev.off()