added lineage_dist.R nad renamed lineage_bp_data file to lineage_data

scripts/functions/lineage_dist.R

@@ -0,0 +1,69 @@
+###############################
+# TASK: function to plot lineage
+# dist plots with or without facet
+# think about color palette
+# for stability
+##############################
+
+#n_colours = length(unique(lin_dist_plot$duet_scaled))
+#my_palette <- colorRampPalette(c(mcsm_red2, mcsm_red1, mcsm_mid, mcsm_blue1, mcsm_blue2))(n = n_colours+1)
+
+
+lineage_distP <- function(plotdf
+                          , x_axis = "duet_scaled"
+                          , y_axis = "lineage_labels"
+                          , x_lab = "DUET"
+                          , with_facet = F
+                          , facet_wrap_var = ""
+                          , fill_categ = "mutation_info_labels"
+                          , fill_categ_cols = c("#E69F00", "#999999")
+                          , my_ats = 15 # axis text size
+                          , my_als = 20 # axis label size
+                          , my_leg_ts = 16
+                          , my_leg_title = 16
+                          , my_strip_ts = 20
+                          , leg_pos = c(0.8, 0.9)
+                          , leg_pos_wf = c("top", "left", "bottom", "right")
+                          , leg_dir_wf = c("horizontal", "vertical")
+                          , leg_label = "")
+
+{
+
+LinDistP = ggplot(plotdf, aes_string(x = x_axis
+                              , y = y_axis))+
+
+  geom_density_ridges(aes_string(fill = fill_categ)
+                      , scale = 3
+                      , size = 0.3
+                      , alpha = 0.8) +
+  scale_x_continuous(expand = c(0.01, 0.01)) +
+  #coord_cartesian( xlim = c(-1, 1)) +
+  scale_fill_manual(values = fill_categ_cols) +
+  theme(axis.text.x = element_text(size = my_ats
+                                   , angle = 90
+                                   , hjust = 1
+                                   , vjust = 0.4)
+        , axis.text.y = element_text(size = my_ats)
+        , axis.title.x = element_text(size = my_ats)
+        , axis.title.y = element_blank()
+        , strip.text = element_text(size = my_strip_ts)
+        , legend.text = element_text(size = my_leg_ts)
+        , legend.title = element_text(size = my_leg_title)
+        , legend.position = c(0.8, 0.9)) +
+  labs(x = x_lab
+       , fill = leg_label)
+
+if (with_facet){
+
+  # used reformulate or make as formula
+  #fwv = reformulate(facet_wrap_var)
+  fwv = as.formula(paste0("~", facet_wrap_var))
+  
+  LinDistP = LinDistP + 
+    facet_wrap(fwv) + 
+    theme(legend.position = leg_pos_wf
+          , legend.direction = leg_dir_wf)
+}
+
+return(LinDistP)
+}