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replaced old lineage barplot with count and diversity combined plots sourced from function

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This commit is contained in:
Tanushree Tunstall 2021-09-07 09:27:47 +01:00
parent 357ceb8920
commit 7dc72fb118
7 changed files with 217 additions and 366 deletions
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112
scripts/plotting/lineage_bp_data.R
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@ -68,42 +68,35 @@ lin_wf
#=====================
# SNP diversity
lin_wf$snp_diversity_f = round( (lin_wf$snp_diversity * 100), digits = 0)
lin_wf
lin_wf$snp_diversity_f = paste0(lin_wf$snp_diversity_f, "%")
# Lineage names
lin_wf$sel_lineages_f = gsub("lineage", "L", lin_wf$sel_lineages)
lin_wf
# # Lineage names
# lin_wf = lin_wf %>%
# mutate(ordering_category = case_when(
# sel_lineages_f == "" ~ 0
# , sel_lineages_f == "L1" ~ 1
# , sel_lineages_f == "L2" ~ 2
# , sel_lineages_f == "L3" ~ 3
# , sel_lineages_f == "L4" ~ 4
# , sel_lineages_f == "L5" ~ 5
# , sel_lineages_f == "L6" ~ 6
# , sel_lineages_f == "L7" ~ 7
# , sel_lineages_f == "LBOV" ~ 8
#
# , sel_lineages_f == "L1;L2" ~ 9
# , sel_lineages_f == "L1;L3" ~ 10
# , sel_lineages_f == "L1;L4" ~ 11
#
# , sel_lineages_f == "L2;L3" ~ 12
# , sel_lineages_f == "L2;L3;L4" ~ 13
# , sel_lineages_f == "L2;L4" ~ 14
# , sel_lineages_f == "L2;L6" ~ 15
# , sel_lineages_f == "L2;LBOV" ~ 16
#
# , sel_lineages_f == "L3;L4" ~ 17
#
# , sel_lineages_f == "L4;L6" ~ 18
# , sel_lineages_f == "L4;L7" ~ 19
#
# , FALSE ~ -1)
# )
# Important: Relevel factors so that x-axis categ appear as you want
lin_wf$sel_lineages_f = factor(lin_wf$sel_lineages_f, c("L1"
, "L2"
, "L3"
, "L4"
, "L5"
, "L6"
, "L7"
, "LBOV"
, "L1;L2"
, "L1;L3"
, "L1;L4"
, "L2;L3"
, "L2;L3;L4"
, "L2;L4"
, "L2;L6"
, "L2;LBOV"
, "L3;L4"
, "L4;L6"
, "L4;L7"
, ""))
levels(lin_wf$sel_lineages_f)
##################################
# LF data: lineages with
@ -134,40 +127,27 @@ if ( nrow(lin_lf) == expected_rows ){
cat("\nFAIL: numbers mismatch"
, "\nExpected nrow: ", expected_rows)
}
#######################################
# #=====================
# # Add some formatting
# #=====================
# lin_lf$sel_lineages_f = gsub("lineage", "L", lin_lf$sel_lineages)
# lin_lf
# Important: Relevel factors so that x-axis categ appear as you want
lin_lf$sel_lineages_f = factor(lin_lf$sel_lineages_f, c("L1"
, "L2"
, "L3"
, "L4"
, "L5"
, "L6"
, "L7"
, "LBOV"
, "L1;L2"
, "L1;L3"
, "L1;L4"
, "L2;L3"
, "L2;L3;L4"
, "L2;L4"
, "L2;L6"
, "L2;LBOV"
, "L3;L4"
, "L4;L6"
, "L4;L7"
, ""))
# lin_lf = lin_lf %>%
# mutate(ordering_category = case_when(
# sel_lineages_f == "" ~ 0
# , sel_lineages_f == "L1" ~ 1
# , sel_lineages_f == "L2" ~ 2
# , sel_lineages_f == "L3" ~ 3
# , sel_lineages_f == "L4" ~ 4
# , sel_lineages_f == "L5" ~ 5
# , sel_lineages_f == "L6" ~ 6
# , sel_lineages_f == "L7" ~ 7
# , sel_lineages_f == "LBOV" ~ 8
#
# , sel_lineages_f == "L1;L2" ~ 9
# , sel_lineages_f == "L1;L3" ~ 10
# , sel_lineages_f == "L1;L4" ~ 11
#
# , sel_lineages_f == "L2;L3" ~ 12
# , sel_lineages_f == "L2;L3;L4" ~ 13
# , sel_lineages_f == "L2;L4" ~ 14
# , sel_lineages_f == "L2;L6" ~ 15
# , sel_lineages_f == "L2;LBOV" ~ 16
#
# , sel_lineages_f == "L3;L4" ~ 17
#
# , sel_lineages_f == "L4;L6" ~ 18
# , sel_lineages_f == "L4;L7" ~ 19
#
# , FALSE ~ -1)
# )
levels(lin_lf$sel_lineages_f)