replaced old lineage barplot with count and diversity combined plots sourced from function
This commit is contained in:
parent
357ceb8920
commit
7dc72fb118
7 changed files with 217 additions and 366 deletions
|
|
@ -20,8 +20,8 @@ lin_count_bp <- function( lf_data
|
||||||
, my_xals = 22 # x axis label size
|
, my_xals = 22 # x axis label size
|
||||||
, my_yals = 22 # y axis label size
|
, my_yals = 22 # y axis label size
|
||||||
, my_lls = 22 # legend label size
|
, my_lls = 22 # legend label size
|
||||||
, bar_col_labels = c("Mutations", "Total Samples")
|
, bar_col_labels = ""
|
||||||
, bar_col_values = c("grey50", "gray75")
|
, bar_col_values = ""
|
||||||
, bar_leg_name = ""
|
, bar_leg_name = ""
|
||||||
, leg_location = "top"
|
, leg_location = "top"
|
||||||
, y_log10 = FALSE
|
, y_log10 = FALSE
|
||||||
|
|
@ -68,20 +68,18 @@ lin_count_bp <- function( lf_data
|
||||||
, y = y_label
|
, y = y_label
|
||||||
, colour = "black")
|
, colour = "black")
|
||||||
|
|
||||||
|
|
||||||
if (y_log10){
|
if (y_log10){
|
||||||
|
|
||||||
OutPlot = OutPlot +
|
OutPlot = OutPlot +
|
||||||
scale_y_continuous(trans = "log10"
|
scale_y_continuous(trans = "log10"
|
||||||
, labels = trans_format("log10", math_format(10^.x) ) )
|
, labels = trans_format("log10", math_format(10^.x) ) )
|
||||||
|
}
|
||||||
}
|
|
||||||
|
|
||||||
if (y_scale_percent){
|
if (y_scale_percent){
|
||||||
|
|
||||||
OutPlot = OutPlot +
|
OutPlot = OutPlot +
|
||||||
#scale_y_continuous(labels = scales::percent_format(accuracy = 1)) +
|
scale_y_continuous(labels = scales::percent_format(accuracy = 1)) +
|
||||||
scale_y_continuous(labels = scales::percent) +
|
#scale_y_continuous(labels = scales::percent) +
|
||||||
|
|
||||||
labs(title = ""
|
labs(title = ""
|
||||||
, x = ""
|
, x = ""
|
||||||
|
|
|
||||||
|
|
@ -1,39 +1,25 @@
|
||||||
setwd("~/git/LSHTM_analysis/scripts/plotting")
|
setwd("~/git/LSHTM_analysis/scripts/plotting")
|
||||||
|
|
||||||
#source ('get_plotting_dfs.R')
|
source ('get_plotting_dfs.R')
|
||||||
source("../functions/bp_lineage.R")
|
source("../functions/bp_lineage.R")
|
||||||
|
|
||||||
#########################################
|
#########################################
|
||||||
# Lineage and SNP count: lineage lf data
|
# Lineage and SNP count: lineage lf data
|
||||||
#########################################
|
#########################################
|
||||||
# Relevel factors so that x-axis categ appear as you want
|
#=========================
|
||||||
lin_lf_plot = lin_lf
|
# Data: All lineages or
|
||||||
lin_lf_plot
|
# selected few
|
||||||
is.factor(lin_lf_plot$sel_lineages_f)
|
#=========================
|
||||||
|
sel_lineages = levels(lin_lf$sel_lineages_f)
|
||||||
lin_lf_plot$sel_lineages_f = factor(lin_lf_plot$sel_lineages_f, c(""
|
sel_lineages
|
||||||
, "L1"
|
lin_lf_plot = lin_lf[lin_lf$sel_lineages_f%in%sel_lineages,]
|
||||||
, "L2"
|
|
||||||
, "L3"
|
|
||||||
, "L4"
|
|
||||||
, "L5"
|
|
||||||
, "L6"
|
|
||||||
, "L7"
|
|
||||||
, "LBOV"
|
|
||||||
, "L1;L2"
|
|
||||||
, "L1;L3"
|
|
||||||
, "L1;L4"
|
|
||||||
, "L2;L3"
|
|
||||||
, "L2;L3;L4"
|
|
||||||
, "L2;L4"
|
|
||||||
, "L2;L6"
|
|
||||||
, "L2;LBOV"
|
|
||||||
, "L3;L4"
|
|
||||||
, "L4;L6"
|
|
||||||
, "L4;L7"))
|
|
||||||
|
|
||||||
|
# drop unused factor levels
|
||||||
|
lin_lf_plot$sel_lineages_f = factor(lin_lf_plot$sel_lineages_f)
|
||||||
levels(lin_lf_plot$sel_lineages_f)
|
levels(lin_lf_plot$sel_lineages_f)
|
||||||
|
#=========================
|
||||||
|
# Lineage count plot
|
||||||
|
#=========================
|
||||||
lin_count_bp(lin_lf_plot
|
lin_count_bp(lin_lf_plot
|
||||||
, x_categ = "sel_lineages_f"
|
, x_categ = "sel_lineages_f"
|
||||||
, y_count = "p_count"
|
, y_count = "p_count"
|
||||||
|
|
@ -44,68 +30,33 @@ lin_count_bp(lin_lf_plot
|
||||||
, my_xats = 20
|
, my_xats = 20
|
||||||
, bar_col_labels = c("Mutations", "Total Samples")
|
, bar_col_labels = c("Mutations", "Total Samples")
|
||||||
, bar_col_values = c("grey50", "gray75")
|
, bar_col_values = c("grey50", "gray75")
|
||||||
, y_log10 = T
|
, y_scale_percent = F # T for diversity
|
||||||
, y_label = "Count"
|
, y_log10 = F
|
||||||
, y_scale_percent = F)
|
, y_label = "Count")
|
||||||
|
|
||||||
###############################################
|
###############################################
|
||||||
# Lineage SNP diversity count: lineage wf data
|
# Lineage SNP diversity count: lineage wf data
|
||||||
###############################################
|
###############################################
|
||||||
# Relevel factors so that x-axis categ appear as you want
|
#=========================
|
||||||
lin_wf_plot = lin_wf
|
# Data: All lineages or
|
||||||
is.factor(lin_wf_plot$sel_lineages_f)
|
# selected few
|
||||||
|
#=========================
|
||||||
lin_wf_plot$sel_lineages_f = factor(lin_wf_plot$sel_lineages_f, c(""
|
sel_lineages = levels(lin_wf$sel_lineages_f)
|
||||||
, "L1"
|
sel_lineages
|
||||||
, "L2"
|
lin_wf_plot = lin_wf[lin_wf$sel_lineages_f%in%sel_lineages,]
|
||||||
, "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"))
|
|
||||||
|
|
||||||
|
# drop unused factor levels
|
||||||
|
lin_wf_plot$sel_lineages_f = factor(lin_wf_plot$sel_lineages_f)
|
||||||
levels(lin_wf_plot$sel_lineages_f)
|
levels(lin_wf_plot$sel_lineages_f)
|
||||||
|
#=========================
|
||||||
#==========
|
# Lineage Diversity plot
|
||||||
# Plot
|
#=========================
|
||||||
#==========
|
|
||||||
lin_count_bp(lin_wf_plot
|
lin_count_bp(lin_wf_plot
|
||||||
, x_categ = "sel_lineages_f"
|
, x_categ = "sel_lineages_f"
|
||||||
, y_count = "snp_diversity"
|
, y_count = "snp_diversity"
|
||||||
, display_label_col = "snp_diversity_f"
|
, display_label_col = "snp_diversity_f"
|
||||||
|
|
||||||
, bar_stat_stype = "identity"
|
, bar_stat_stype = "identity"
|
||||||
, x_lab_angle = 90
|
, x_lab_angle = 90
|
||||||
, my_xats = 20
|
, my_xats = 20
|
||||||
, y_scale_percent = T
|
, y_scale_percent = T
|
||||||
, y_label = "SNP diversity"
|
, 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
|
|
||||||
|
|
|
||||||
|
|
@ -23,7 +23,7 @@ plot_basic_bp_combined_labelled = paste0(plotdir,"/", basic_bp_combined_labell
|
||||||
|
|
||||||
#=======================================================================
|
#=======================================================================
|
||||||
#=======
|
#=======
|
||||||
# combin DUET and Ligand affinity plots
|
# combine DUET and Ligand affinity plots
|
||||||
#=======
|
#=======
|
||||||
svg(plot_basic_bp_combined_labelled , width = 12, height = 12 )
|
svg(plot_basic_bp_combined_labelled , width = 12, height = 12 )
|
||||||
|
|
||||||
|
|
|
||||||
|
|
@ -1,214 +0,0 @@
|
||||||
#!/usr/bin/env Rscript
|
|
||||||
getwd()
|
|
||||||
setwd("~/git/LSHTM_analysis/scripts/plotting/")
|
|
||||||
getwd()
|
|
||||||
#########################################################
|
|
||||||
# TASK: Basic lineage barplot showing numbers
|
|
||||||
|
|
||||||
# Output: Basic barplot with lineage samples and mut count
|
|
||||||
|
|
||||||
##########################################################
|
|
||||||
# Installing and loading required packages
|
|
||||||
##########################################################
|
|
||||||
source("Header_TT.R")
|
|
||||||
require(data.table)
|
|
||||||
source("combining_dfs_plotting.R")
|
|
||||||
# should return the following dfs, directories and variables
|
|
||||||
|
|
||||||
# PS combined:
|
|
||||||
# 1) merged_df2
|
|
||||||
# 2) merged_df2_comp
|
|
||||||
# 3) merged_df3
|
|
||||||
# 4) merged_df3_comp
|
|
||||||
|
|
||||||
# LIG combined:
|
|
||||||
# 5) merged_df2_lig
|
|
||||||
# 6) merged_df2_comp_lig
|
|
||||||
# 7) merged_df3_lig
|
|
||||||
# 8) merged_df3_comp_lig
|
|
||||||
|
|
||||||
# 9) my_df_u
|
|
||||||
# 10) my_df_u_lig
|
|
||||||
|
|
||||||
cat("Directories imported:"
|
|
||||||
, "\n===================="
|
|
||||||
, "\ndatadir:", datadir
|
|
||||||
, "\nindir:", indir
|
|
||||||
, "\noutdir:", outdir
|
|
||||||
, "\nplotdir:", plotdir)
|
|
||||||
|
|
||||||
cat("Variables imported:"
|
|
||||||
, "\n====================="
|
|
||||||
, "\ndrug:", drug
|
|
||||||
, "\ngene:", gene
|
|
||||||
, "\ngene_match:", gene_match
|
|
||||||
, "\nAngstrom symbol:", angstroms_symbol
|
|
||||||
, "\nNo. of duplicated muts:", dup_muts_nu
|
|
||||||
, "\nNA count for ORs:", na_count
|
|
||||||
, "\nNA count in df2:", na_count_df2
|
|
||||||
, "\nNA count in df3:", na_count_df3
|
|
||||||
, "\ndr_muts_col:", dr_muts_col
|
|
||||||
, "\nother_muts_col:", other_muts_col
|
|
||||||
, "\ndrtype_col:", resistance_col)
|
|
||||||
|
|
||||||
|
|
||||||
#===========
|
|
||||||
# input
|
|
||||||
#===========
|
|
||||||
# output of combining_dfs_plotting.R
|
|
||||||
|
|
||||||
#=======
|
|
||||||
# output
|
|
||||||
#=======
|
|
||||||
# plot 1
|
|
||||||
basic_bp_lineage = "basic_lineage_barplot.svg"
|
|
||||||
plot_basic_bp_lineage = paste0(plotdir,"/", basic_bp_lineage)
|
|
||||||
|
|
||||||
#=======================================================================
|
|
||||||
#================
|
|
||||||
# Data for plots:
|
|
||||||
# you need merged_df2, comprehensive one
|
|
||||||
# since this has one-many relationship
|
|
||||||
# i.e the same SNP can belong to multiple lineages
|
|
||||||
#================
|
|
||||||
# REASSIGNMENT as necessary
|
|
||||||
my_df = merged_df2
|
|
||||||
|
|
||||||
# clear excess variable
|
|
||||||
rm(merged_df2_comp, merged_df3, merged_df3_comp)
|
|
||||||
|
|
||||||
# quick checks
|
|
||||||
colnames(my_df)
|
|
||||||
str(my_df)
|
|
||||||
|
|
||||||
# Ensure correct data type in columns to plot: need to be factor
|
|
||||||
is.factor(my_df$lineage)
|
|
||||||
my_df$lineage = as.factor(my_df$lineage)
|
|
||||||
is.factor(my_df$lineage)
|
|
||||||
|
|
||||||
#==========================
|
|
||||||
# Plot: Lineage barplot
|
|
||||||
# x = lineage y = No. of samples
|
|
||||||
# col = Lineage
|
|
||||||
# fill = lineage
|
|
||||||
#============================
|
|
||||||
table(my_df$lineage)
|
|
||||||
as.data.frame(table(my_df$lineage))
|
|
||||||
|
|
||||||
#=============
|
|
||||||
# Data for plots
|
|
||||||
#=============
|
|
||||||
# REASSIGNMENT
|
|
||||||
df <- my_df
|
|
||||||
|
|
||||||
rm(my_df)
|
|
||||||
|
|
||||||
# get freq count of positions so you can subset freq<1
|
|
||||||
#setDT(df)[, lineage_count := .N, by = .(lineage)]
|
|
||||||
|
|
||||||
#******************
|
|
||||||
# generate plot: barplot of mutation by lineage
|
|
||||||
#******************
|
|
||||||
sel_lineages = c("lineage1"
|
|
||||||
, "lineage2"
|
|
||||||
, "lineage3"
|
|
||||||
, "lineage4"
|
|
||||||
#, "lineage5"
|
|
||||||
#, "lineage6"
|
|
||||||
#, "lineage7"
|
|
||||||
)
|
|
||||||
|
|
||||||
df_lin = subset(df, subset = lineage %in% sel_lineages)
|
|
||||||
|
|
||||||
# Create df with lineage inform & no. of unique mutations
|
|
||||||
# per lineage and total samples within lineage
|
|
||||||
# this is essentially barplot with two y axis
|
|
||||||
|
|
||||||
bar = bar = as.data.frame(sel_lineages) #4, 1
|
|
||||||
total_snps_u = NULL
|
|
||||||
total_samples = NULL
|
|
||||||
|
|
||||||
for (i in sel_lineages){
|
|
||||||
#print(i)
|
|
||||||
curr_total = length(unique(df$id)[df$lineage==i])
|
|
||||||
total_samples = c(total_samples, curr_total)
|
|
||||||
print(total_samples)
|
|
||||||
|
|
||||||
foo = df[df$lineage==i,]
|
|
||||||
print(paste0(i, "======="))
|
|
||||||
print(length(unique(foo$mutationinformation)))
|
|
||||||
curr_count = length(unique(foo$mutationinformation))
|
|
||||||
|
|
||||||
total_snps_u = c(total_snps_u, curr_count)
|
|
||||||
}
|
|
||||||
|
|
||||||
print(total_snps_u)
|
|
||||||
bar$num_snps_u = total_snps_u
|
|
||||||
bar$total_samples = total_samples
|
|
||||||
bar
|
|
||||||
|
|
||||||
#*****************
|
|
||||||
# generate plot: lineage barplot with two y-axis
|
|
||||||
#https://stackoverflow.com/questions/13035295/overlay-bar-graphs-in-ggplot2
|
|
||||||
#*****************
|
|
||||||
|
|
||||||
y1 = bar$num_snps_u
|
|
||||||
y2 = bar$total_samples
|
|
||||||
x = sel_lineages
|
|
||||||
|
|
||||||
to_plot = data.frame(x = x
|
|
||||||
, y1 = y1
|
|
||||||
, y2 = y2)
|
|
||||||
to_plot
|
|
||||||
|
|
||||||
# FIXME later: will be depricated!
|
|
||||||
melted = melt(to_plot, id = "x")
|
|
||||||
melted
|
|
||||||
|
|
||||||
|
|
||||||
svg(plot_basic_bp_lineage)
|
|
||||||
|
|
||||||
my_ats = 20 # axis text size
|
|
||||||
my_als = 22 # axis label size
|
|
||||||
|
|
||||||
g = ggplot(melted, aes(x = x
|
|
||||||
, y = value
|
|
||||||
, fill = variable))
|
|
||||||
|
|
||||||
printFile = g + geom_bar(stat = "identity"
|
|
||||||
, position = position_stack(reverse = TRUE)
|
|
||||||
, alpha=.75
|
|
||||||
, colour='grey75') +
|
|
||||||
theme(axis.text.x = element_text(size = my_ats)
|
|
||||||
, axis.text.y = element_text(size = my_ats
|
|
||||||
#, angle = 30
|
|
||||||
, hjust = 1
|
|
||||||
, vjust = 0)
|
|
||||||
, axis.title.x = element_text(size = my_als
|
|
||||||
, colour = 'black')
|
|
||||||
, axis.title.y = element_text(size = my_als
|
|
||||||
, colour = 'black')
|
|
||||||
, legend.position = "top"
|
|
||||||
, legend.text = element_text(size = my_als)) +
|
|
||||||
#geom_text() +
|
|
||||||
geom_label(aes(label = value)
|
|
||||||
, size = 5
|
|
||||||
, hjust = 0.5
|
|
||||||
, vjust = 0.5
|
|
||||||
, colour = 'black'
|
|
||||||
, show.legend = FALSE
|
|
||||||
#, check_overlap = TRUE
|
|
||||||
, position = position_stack(reverse = T)) +
|
|
||||||
labs(title = ''
|
|
||||||
, x = ''
|
|
||||||
, y = "Number"
|
|
||||||
, fill = 'Variable'
|
|
||||||
, colour = 'black') +
|
|
||||||
scale_fill_manual(values = c('grey50', 'gray75')
|
|
||||||
, name=''
|
|
||||||
, labels=c('Mutations', 'Total Samples')) +
|
|
||||||
scale_x_discrete(breaks = c('lineage1', 'lineage2', 'lineage3', 'lineage4')
|
|
||||||
, labels = c('Lineage 1', 'Lineage 2', 'Lineage 3', 'Lineage 4'))
|
|
||||||
|
|
||||||
print(printFile)
|
|
||||||
dev.off()
|
|
||||||
128
scripts/plotting/lineage_basic_barplots_combined.R
Normal file
128
scripts/plotting/lineage_basic_barplots_combined.R
Normal file
|
|
@ -0,0 +1,128 @@
|
||||||
|
#!/usr/bin/env Rscript
|
||||||
|
getwd()
|
||||||
|
setwd("~/git/LSHTM_analysis/scripts/plotting/")
|
||||||
|
getwd()
|
||||||
|
#########################################################
|
||||||
|
# TASK: Basic lineage barplot showing numbers
|
||||||
|
|
||||||
|
# Output: Basic barplot with lineage samples and mut count
|
||||||
|
|
||||||
|
##########################################################
|
||||||
|
# Installing and loading required packages
|
||||||
|
##########################################################
|
||||||
|
source("Header_TT.R")
|
||||||
|
source("../functions/bp_lineage.R")
|
||||||
|
|
||||||
|
#===========
|
||||||
|
# input
|
||||||
|
#===========
|
||||||
|
source ('get_plotting_dfs.R')
|
||||||
|
|
||||||
|
cat("Directories imported:"
|
||||||
|
, "\n===================="
|
||||||
|
, "\ndatadir:", datadir
|
||||||
|
, "\nindir:", indir
|
||||||
|
, "\noutdir:", outdir
|
||||||
|
, "\nplotdir:", plotdir)
|
||||||
|
|
||||||
|
cat("Variables imported:"
|
||||||
|
, "\n====================="
|
||||||
|
, "\ndrug:", drug
|
||||||
|
, "\ngene:", gene
|
||||||
|
, "\ngene_match:", gene_match
|
||||||
|
, "\nAngstrom symbol:", angstroms_symbol
|
||||||
|
#, "\nNo. of duplicated muts:", dup_muts_nu
|
||||||
|
, "\ndr_muts_col:", dr_muts_col
|
||||||
|
, "\nother_muts_col:", other_muts_col
|
||||||
|
, "\ndrtype_col:", resistance_col)
|
||||||
|
|
||||||
|
#=======
|
||||||
|
# output
|
||||||
|
#=======
|
||||||
|
# plot 1
|
||||||
|
basic_bp_lineage_cl = "basic_lineage_barplots_combined.svg"
|
||||||
|
plot_basic_bp_lineage_cl = paste0(plotdir,"/", basic_bp_lineage_cl)
|
||||||
|
plot_basic_bp_lineage_cl
|
||||||
|
#################################################################
|
||||||
|
#=============================
|
||||||
|
# PLOT 1: Lineage count plot:
|
||||||
|
# LF data
|
||||||
|
#=============================
|
||||||
|
#------------------------
|
||||||
|
# Data: All lineages or
|
||||||
|
# selected few
|
||||||
|
#------------------------
|
||||||
|
sel_lineages = levels(lin_lf$sel_lineages_f)[1:4]
|
||||||
|
sel_lineages
|
||||||
|
lin_lf_plot = lin_lf[lin_lf$sel_lineages_f%in%sel_lineages,]
|
||||||
|
str(lin_lf_plot)
|
||||||
|
|
||||||
|
# drop unused factor levels
|
||||||
|
lin_lf_plot$sel_lineages_f = factor(lin_lf_plot$sel_lineages_f)
|
||||||
|
levels(lin_lf_plot$sel_lineages_f)
|
||||||
|
str(lin_lf_plot)
|
||||||
|
|
||||||
|
#------------------------
|
||||||
|
# plot from my function:
|
||||||
|
#------------------------
|
||||||
|
lin_countP = lin_count_bp(lin_lf_plot
|
||||||
|
, 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 = 20
|
||||||
|
, bar_col_labels = c("Mutations", "Total Samples")
|
||||||
|
, bar_col_values = c("grey50", "gray75")
|
||||||
|
, y_scale_percent = F # T for diversity
|
||||||
|
, y_log10 = F
|
||||||
|
, y_label = "Count")
|
||||||
|
lin_countP
|
||||||
|
#================================
|
||||||
|
# PLOT 2: Lineage Diversity plot
|
||||||
|
# WF data
|
||||||
|
#================================
|
||||||
|
#------------------------
|
||||||
|
# Data: All lineages or
|
||||||
|
# selected few
|
||||||
|
#------------------------
|
||||||
|
sel_lineages = levels(lin_wf$sel_lineages_f)[1:4]
|
||||||
|
sel_lineages
|
||||||
|
lin_wf_plot = lin_wf[lin_wf$sel_lineages_f%in%sel_lineages,]
|
||||||
|
str(lin_wf_plot)
|
||||||
|
|
||||||
|
# drop unused factor levels
|
||||||
|
lin_wf_plot$sel_lineages_f = factor(lin_wf_plot$sel_lineages_f)
|
||||||
|
levels(lin_wf_plot$sel_lineages_f)
|
||||||
|
str(lin_wf_plot)
|
||||||
|
|
||||||
|
#------------------------
|
||||||
|
# plot from my function:
|
||||||
|
#------------------------
|
||||||
|
lin_diversityP = lin_count_bp(lin_wf_plot
|
||||||
|
, x_categ = "sel_lineages_f"
|
||||||
|
, y_count = "snp_diversity"
|
||||||
|
, display_label_col = "snp_diversity_f"
|
||||||
|
, bar_stat_stype = "identity"
|
||||||
|
, x_lab_angle = 90
|
||||||
|
, my_xats = 20
|
||||||
|
, y_scale_percent = T
|
||||||
|
, y_label = "SNP diversity")
|
||||||
|
|
||||||
|
lin_diversityP
|
||||||
|
#########################################################################333
|
||||||
|
#================================
|
||||||
|
# Combine plots
|
||||||
|
#================================
|
||||||
|
|
||||||
|
svg(plot_basic_bp_lineage_cl , width = 8, height = 15 )
|
||||||
|
|
||||||
|
lineage_bp_combined = cowplot::plot_grid(lin_countP, lin_diversityP
|
||||||
|
#, labels = c("(a)", "(b)", "(c)", "(d)")
|
||||||
|
, nrow = 2
|
||||||
|
, labels = "AUTO"
|
||||||
|
, label_size = 25)
|
||||||
|
|
||||||
|
lineage_bp_combined
|
||||||
|
dev.off()
|
||||||
|
|
@ -68,42 +68,35 @@ lin_wf
|
||||||
#=====================
|
#=====================
|
||||||
# SNP diversity
|
# SNP diversity
|
||||||
lin_wf$snp_diversity_f = round( (lin_wf$snp_diversity * 100), digits = 0)
|
lin_wf$snp_diversity_f = round( (lin_wf$snp_diversity * 100), digits = 0)
|
||||||
lin_wf
|
lin_wf$snp_diversity_f = paste0(lin_wf$snp_diversity_f, "%")
|
||||||
|
|
||||||
# Lineage names
|
# Lineage names
|
||||||
lin_wf$sel_lineages_f = gsub("lineage", "L", lin_wf$sel_lineages)
|
lin_wf$sel_lineages_f = gsub("lineage", "L", lin_wf$sel_lineages)
|
||||||
lin_wf
|
lin_wf
|
||||||
|
|
||||||
# # Lineage names
|
# Important: Relevel factors so that x-axis categ appear as you want
|
||||||
# lin_wf = lin_wf %>%
|
lin_wf$sel_lineages_f = factor(lin_wf$sel_lineages_f, c("L1"
|
||||||
# mutate(ordering_category = case_when(
|
, "L2"
|
||||||
# sel_lineages_f == "" ~ 0
|
, "L3"
|
||||||
# , sel_lineages_f == "L1" ~ 1
|
, "L4"
|
||||||
# , sel_lineages_f == "L2" ~ 2
|
, "L5"
|
||||||
# , sel_lineages_f == "L3" ~ 3
|
, "L6"
|
||||||
# , sel_lineages_f == "L4" ~ 4
|
, "L7"
|
||||||
# , sel_lineages_f == "L5" ~ 5
|
, "LBOV"
|
||||||
# , sel_lineages_f == "L6" ~ 6
|
, "L1;L2"
|
||||||
# , sel_lineages_f == "L7" ~ 7
|
, "L1;L3"
|
||||||
# , sel_lineages_f == "LBOV" ~ 8
|
, "L1;L4"
|
||||||
#
|
, "L2;L3"
|
||||||
# , sel_lineages_f == "L1;L2" ~ 9
|
, "L2;L3;L4"
|
||||||
# , sel_lineages_f == "L1;L3" ~ 10
|
, "L2;L4"
|
||||||
# , sel_lineages_f == "L1;L4" ~ 11
|
, "L2;L6"
|
||||||
#
|
, "L2;LBOV"
|
||||||
# , sel_lineages_f == "L2;L3" ~ 12
|
, "L3;L4"
|
||||||
# , sel_lineages_f == "L2;L3;L4" ~ 13
|
, "L4;L6"
|
||||||
# , sel_lineages_f == "L2;L4" ~ 14
|
, "L4;L7"
|
||||||
# , sel_lineages_f == "L2;L6" ~ 15
|
, ""))
|
||||||
# , sel_lineages_f == "L2;LBOV" ~ 16
|
|
||||||
#
|
levels(lin_wf$sel_lineages_f)
|
||||||
# , sel_lineages_f == "L3;L4" ~ 17
|
|
||||||
#
|
|
||||||
# , sel_lineages_f == "L4;L6" ~ 18
|
|
||||||
# , sel_lineages_f == "L4;L7" ~ 19
|
|
||||||
#
|
|
||||||
# , FALSE ~ -1)
|
|
||||||
# )
|
|
||||||
|
|
||||||
##################################
|
##################################
|
||||||
# LF data: lineages with
|
# LF data: lineages with
|
||||||
|
|
@ -134,40 +127,27 @@ if ( nrow(lin_lf) == expected_rows ){
|
||||||
cat("\nFAIL: numbers mismatch"
|
cat("\nFAIL: numbers mismatch"
|
||||||
, "\nExpected nrow: ", expected_rows)
|
, "\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 %>%
|
levels(lin_lf$sel_lineages_f)
|
||||||
# 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)
|
|
||||||
# )
|
|
||||||
|
|
|
||||||
|
|
@ -112,6 +112,14 @@ note:
|
||||||
- fa flag has default if not supplied
|
- fa flag has default if not supplied
|
||||||
- fb flag has default if not supplied
|
- fb flag has default if not supplied
|
||||||
|
|
||||||
|
|
||||||
|
#===================
|
||||||
|
# Add LINEAGE ONE
|
||||||
|
#===================
|
||||||
|
# Lineage_bp.R
|
||||||
|
creates Count and Diversity plot
|
||||||
|
|
||||||
|
|
||||||
########################################################################
|
########################################################################
|
||||||
# TODO
|
# TODO
|
||||||
Delete: dirs.R
|
Delete: dirs.R
|
||||||
|
|
|
||||||
Loading…
Add table
Add a link
Reference in a new issue