From 56a6aa8c7eb77b5ec16af855c1a7140f28ae094d Mon Sep 17 00:00:00 2001 From: Tanushree Tunstall Date: Sun, 6 Mar 2022 13:31:43 +0000 Subject: [PATCH] lineage_dist: add all_lineages feature --- scripts/functions/bp_lineage_diversity.R | 3 ++- scripts/functions/lineage_dist.R | 6 ++++++ 2 files changed, 8 insertions(+), 1 deletion(-) diff --git a/scripts/functions/bp_lineage_diversity.R b/scripts/functions/bp_lineage_diversity.R index 40a7210..cfa1fb6 100644 --- a/scripts/functions/bp_lineage_diversity.R +++ b/scripts/functions/bp_lineage_diversity.R @@ -5,9 +5,10 @@ ######################################## lin_count_bp_diversity <- function( lf_data = lin_wf + , all_lineages = F , x_categ = "sel_lineages" , y_count = "snp_diversity" - , all_lineages = F + #, all_lineages = F , use_lineages = c("L1", "L2", "L3", "L4") #, bar_fill_categ = "count_categ" , display_label_col = "snp_diversity_f" diff --git a/scripts/functions/lineage_dist.R b/scripts/functions/lineage_dist.R index aee1b62..0ea221f 100644 --- a/scripts/functions/lineage_dist.R +++ b/scripts/functions/lineage_dist.R @@ -13,6 +13,8 @@ lineage_distP <- function(plotdf , x_axis = "duet_scaled" , y_axis = "lineage_labels" , x_lab = "DUET" + , all_lineages = F + , use_lineages = c("L1", "L2", "L3", "L4") , with_facet = F , facet_wrap_var = "" , fill_categ = "mutation_info_labels" @@ -29,6 +31,10 @@ lineage_distP <- function(plotdf { +if(!all_lineages){ + plotdf = plotdf[plotdf[[y_axis]]%in%use_lineages,] +} + LinDistP = ggplot(plotdf, aes_string(x = x_axis , y = y_axis))+