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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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12
scripts/functions/bp_lineage.R
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@ -20,8 +20,8 @@ lin_count_bp <- function( lf_data
, my_xals = 22 # x axis label size
, my_yals = 22 # y axis label size
, my_lls = 22 # legend label size
, bar_col_labels = c("Mutations", "Total Samples")
, bar_col_values = c("grey50", "gray75")
, bar_col_labels = ""
, bar_col_values = ""
, bar_leg_name = ""
, leg_location = "top"
, y_log10 = FALSE
@ -68,20 +68,18 @@ lin_count_bp <- function( lf_data
, y = y_label
, colour = "black")
if (y_log10){
OutPlot = OutPlot +
scale_y_continuous(trans = "log10"
, labels = trans_format("log10", math_format(10^.x) ) )
}
}
if (y_scale_percent){
OutPlot = OutPlot +
#scale_y_continuous(labels = scales::percent_format(accuracy = 1)) +
scale_y_continuous(labels = scales::percent) +
scale_y_continuous(labels = scales::percent_format(accuracy = 1)) +
#scale_y_continuous(labels = scales::percent) +
labs(title = ""
, x = ""

107
scripts/functions/test_bp_lineage.R
View file

@ -1,39 +1,25 @@
setwd("~/git/LSHTM_analysis/scripts/plotting")
#source ('get_plotting_dfs.R')
source ('get_plotting_dfs.R')
source("../functions/bp_lineage.R")
#########################################
# Lineage and SNP count: lineage lf data
#########################################
# Relevel factors so that x-axis categ appear as you want
lin_lf_plot = lin_lf
lin_lf_plot
is.factor(lin_lf_plot$sel_lineages_f)
lin_lf_plot$sel_lineages_f = factor(lin_lf_plot$sel_lineages_f, c(""
, "L1"
, "L2"
, "L3"
, "L4"
, "L5"
, "L6"
, "L7"
, "LBOV"
, "L1;L2"
, "L1;L3"
, "L1;L4"
, "L2;L3"
, "L2;L3;L4"
, "L2;L4"
, "L2;L6"
, "L2;LBOV"
, "L3;L4"
, "L4;L6"
, "L4;L7"))
#=========================
# Data: All lineages or
# selected few
#=========================
sel_lineages = levels(lin_lf$sel_lineages_f)
sel_lineages
lin_lf_plot = lin_lf[lin_lf$sel_lineages_f%in%sel_lineages,]
# drop unused factor levels
lin_lf_plot$sel_lineages_f = factor(lin_lf_plot$sel_lineages_f)
levels(lin_lf_plot$sel_lineages_f)
#=========================
# Lineage count plot
#=========================
lin_count_bp(lin_lf_plot
, x_categ = "sel_lineages_f"
, y_count = "p_count"
@ -44,68 +30,33 @@ lin_count_bp(lin_lf_plot
, my_xats = 20
, bar_col_labels = c("Mutations", "Total Samples")
, bar_col_values = c("grey50", "gray75")
, y_log10 = T
, y_label = "Count"
, y_scale_percent = F)
, y_scale_percent = F # T for diversity
, y_log10 = F
, y_label = "Count")
###############################################
# Lineage SNP diversity count: lineage wf data
###############################################
# Relevel factors so that x-axis categ appear as you want
lin_wf_plot = lin_wf
is.factor(lin_wf_plot$sel_lineages_f)
lin_wf_plot$sel_lineages_f = factor(lin_wf_plot$sel_lineages_f, c(""
, "L1"
, "L2"
, "L3"
, "L4"
, "L5"
, "L6"
, "L7"
, "LBOV"
, "L1;L2"
, "L1;L3"
, "L1;L4"
, "L2;L3"
, "L2;L3;L4"
, "L2;L4"
, "L2;L6"
, "L2;LBOV"
, "L3;L4"
, "L4;L6"
, "L4;L7"))
#=========================
# Data: All lineages or
# selected few
#=========================
sel_lineages = levels(lin_wf$sel_lineages_f)
sel_lineages
lin_wf_plot = lin_wf[lin_wf$sel_lineages_f%in%sel_lineages,]
# drop unused factor levels
lin_wf_plot$sel_lineages_f = factor(lin_wf_plot$sel_lineages_f)
levels(lin_wf_plot$sel_lineages_f)
#==========
# Plot
#==========
#=========================
# Lineage Diversity plot
#=========================
lin_count_bp(lin_wf_plot
, x_categ = "sel_lineages_f"
, y_count = "snp_diversity"
, display_label_col = "snp_diversity_f"
, bar_stat_stype = "identity"
, x_lab_angle = 90
, my_xats = 20
, y_scale_percent = T
, y_label = "SNP diversity"
)
, x_categ = "sel_lineages_f"
, y_count = "p_count"
, bar_fill_categ = "count_categ"
, display_label_col = "p_count"
, bar_stat_stype = "identity"
, x_lab_angle = 90
, my_xats = 15
, bar_col_labels = c("Mutations", "Total Samples")
, bar_col_values = c("grey50", "gray75")
, y_log10 = T
, y_scale_percent = F
, y_label = "SNP diversity")