100 lines
3.9 KiB
R
100 lines
3.9 KiB
R
########################################
|
|
# Lineage barplot
|
|
# Lineage and nsSNP count barplot
|
|
# Lineage Diversity barplot
|
|
########################################
|
|
|
|
lin_count_bp_diversity <- function( lf_data = lin_wf
|
|
, all_lineages = F
|
|
, x_categ = "sel_lineages"
|
|
, y_count = "snp_diversity"
|
|
#, all_lineages = F
|
|
, use_lineages = c("L1", "L2", "L3", "L4")
|
|
#, bar_fill_categ = "count_categ"
|
|
, display_label_col = "snp_diversity_f"
|
|
, bar_stat_stype = "identity"
|
|
, x_lab_angle = 90
|
|
, d_lab_size = 5
|
|
, d_lab_hjust = 0.5
|
|
, d_lab_vjust = 0.5
|
|
, d_lab_col = "black"
|
|
, my_xats = 20 # x axis text size
|
|
, my_yats = 20 # y axis text size
|
|
, 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_leg_name = ""
|
|
, leg_location = "top"
|
|
, y_log10 = FALSE
|
|
, y_scale_percent = FALSE
|
|
#, y_label = c("Count", "SNP diversity")
|
|
, y_label = c("SNP diversity")
|
|
) {
|
|
if(!all_lineages){
|
|
lf_data = lf_data[lf_data[[x_categ]]%in%use_lineages,]
|
|
}
|
|
|
|
g = ggplot(lf_data
|
|
, aes( x = factor( eval(parse(text = x_categ)), ordered = T )
|
|
, y = eval(parse(text = y_count))
|
|
#, fill = eval(parse(text = bar_fill_categ))
|
|
) )
|
|
|
|
OutPlot = g + geom_bar( stat = bar_stat_stype
|
|
, position = position_stack(reverse = TRUE)
|
|
#, alpha = 1
|
|
#, colour = "grey75"
|
|
) +
|
|
theme(axis.text.x = element_text(size = my_xats
|
|
, angle = x_lab_angle)
|
|
, axis.text.y = element_text(size = my_yats
|
|
, angle = 90
|
|
, hjust = 1
|
|
, vjust = 0)
|
|
, axis.title.x = element_text(size = my_xals
|
|
, colour = "black")
|
|
, axis.title.y = element_text(size = my_yals
|
|
, colour = "black")
|
|
, legend.position = leg_location
|
|
, legend.text = element_text(size = my_lls)) +
|
|
|
|
geom_label(aes(label = eval(parse(text = display_label_col)))
|
|
, size = d_lab_size
|
|
, hjust = d_lab_hjust
|
|
, vjust = d_lab_vjust
|
|
, colour = d_lab_col
|
|
, show.legend = FALSE
|
|
#, check_overlap = TRUE
|
|
, position = position_stack(reverse = T)) +
|
|
|
|
scale_fill_manual(values = bar_col_values
|
|
, name = bar_leg_name
|
|
, labels = bar_col_labels) +
|
|
labs(title = ""
|
|
, x = ""
|
|
, 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) +
|
|
|
|
labs(title = ""
|
|
, x = ""
|
|
, y = y_label
|
|
, colour = "black")
|
|
}
|
|
|
|
return(OutPlot)
|
|
}
|