added function for generating lineage barplots and also test script along wiadding script for processing data and added it to get_plotting_dfs.R
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6 changed files with 470 additions and 5 deletions
172
scripts/functions/bp_lineage.R
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172
scripts/functions/bp_lineage.R
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########################################
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# Lineage and within SNP count barplot
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########################################
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lin_count_bp <- function( lf_data
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, x_categ = ""
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, y_count = ""
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, bar_fill_categ = ""
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, display_label_col = ""
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, bar_stat_stype = "identity"
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, x_lab_angle = 90
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, d_lab_size = 5
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, d_lab_hjust = 0.5
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, d_lab_vjust = 0.5
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, d_lab_col = "black"
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, my_xats = 20 # x axis text size
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, my_yats = 20 # y axis text size
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, my_xals = 22 # x axis label size
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, my_yals = 22 # y axis label size
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, my_lls = 22 # legend label size
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, bar_col_labels = c("Mutations", "Total Samples")
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, bar_col_values = c("grey50", "gray75")
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, bar_leg_name = ""
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, leg_location = "top"
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, y_log10 = FALSE
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, y_scale_percent = FALSE
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, y_label = c("Count", "SNP diversity")
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) {
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g = ggplot(lf_data
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, aes( x = factor( eval(parse(text = x_categ)), ordered = T )
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, y = eval(parse(text = y_count))
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, fill = eval(parse(text = bar_fill_categ)) ) )
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OutPlot = g + geom_bar( stat = bar_stat_stype
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, position = position_stack(reverse = TRUE)
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#, alpha = 1
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#, colour = "grey75"
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) +
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theme(axis.text.x = element_text(size = my_xats
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, angle = x_lab_angle)
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, axis.text.y = element_text(size = my_yats
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, angle = 90
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, hjust = 1
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, vjust = 0)
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, axis.title.x = element_text(size = my_xals
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, colour = "black")
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, axis.title.y = element_text(size = my_yals
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, colour = "black")
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, legend.position = leg_location
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, legend.text = element_text(size = my_lls)) +
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geom_label(aes(label = eval(parse(text = display_label_col)))
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, size = d_lab_size
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, hjust = d_lab_hjust
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, vjust = d_lab_vjust
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, colour = d_lab_col
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, show.legend = FALSE
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#, check_overlap = TRUE
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, position = position_stack(reverse = T)) +
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scale_fill_manual(values = bar_col_values
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, name = bar_leg_name
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, labels = bar_col_labels) +
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labs(title = ""
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, x = ""
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, y = y_label
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, colour = "black")
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if (y_log10){
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OutPlot = OutPlot +
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scale_y_continuous(trans = "log10"
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, labels = trans_format("log10", math_format(10^.x) ) )
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}
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if (y_scale_percent){
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OutPlot = OutPlot +
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#scale_y_continuous(labels = scales::percent_format(accuracy = 1)) +
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scale_y_continuous(labels = scales::percent) +
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labs(title = ""
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, x = ""
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, y = y_label
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, colour = "black")
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}
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return(OutPlot)
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}
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############################
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# Lineage diversity barplot
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############################
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# lin_diversity_bp <- function( wf_data
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# , x_categ = "sel_lineages"
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# , y_count = "snp_diversity"
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# , bar_stat_stype = "identity"
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# , display_label_col = "snp_diversity_f"
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# , x_lab_angle = 90
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# , d_lab_size = 5
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# , d_lab_hjust = 0.5
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# , d_lab_vjust = 0.5
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# , d_lab_col = "black"
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# , my_xats = 20 # x axis text size
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# , my_yats = 20 # y axis text size
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# , my_xals = 22 # x axis label size
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# , my_yals = 22 # y axis label size
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# , my_lls = 22 # legend label size
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# , bar_leg_name = ""
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# , leg_location = "top"
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# , y_scale_percent = TRUE
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# , y_label = "SNP diversity" )
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#
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# {
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# g = ggplot(wf_data
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# , aes( x = factor( eval(parse(text = x_categ)), ordered = T )
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# , y = eval(parse(text = y_count)) ) )
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#
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# OutPlot = g + geom_bar( stat = bar_stat_stype
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# , position = position_stack(reverse = TRUE)
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# ) +
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#
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# theme(axis.text.x = element_text(size = my_xats
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# , angle = x_lab_angle)
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# , axis.text.y = element_text(size = my_yats
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# , angle = 90
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# , hjust = 1
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# , vjust = 0)
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# , axis.title.x = element_text(size = my_xals
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# , colour = "black")
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# , axis.title.y = element_text(size = my_yals
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# , colour = "black")
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# , legend.position = leg_location
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# , legend.text = element_text(size = my_lls)) +
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#
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# geom_label(aes(label = eval(parse(text = display_label_col)))
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# , size = d_lab_size
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# , hjust = d_lab_hjust
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# , vjust = d_lab_vjust
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# , colour = d_lab_col
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# , show.legend = FALSE
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# #, check_overlap = TRUE
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# , position = position_stack(reverse = T))
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# # return(OutPlot)
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#
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# if (y_scale_percent){
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#
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# OutPlot = OutPlot +
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# scale_y_continuous(labels = scales::percent_format(accuracy = 1)) +
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# labs(title = ""
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# , x = ""
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# , y = y_label
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# , colour = "black")
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#
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# return(OutPlot)
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# }
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# return(OutPlot)
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# }
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# ggp <- ggplot(bar_sel, aes(sel_lineages, snp_diversity)) +
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# geom_bar(stat = "identity")
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# ggp + scale_y_continuous(labels = scales::percent_format(accuracy = 1)
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# #, limits = c(0,1)
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# , breaks = seq(0, 30, 5)
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# )
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111
scripts/functions/test_bp_lineage.R
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111
scripts/functions/test_bp_lineage.R
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setwd("~/git/LSHTM_analysis/scripts/plotting")
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#source ('get_plotting_dfs.R')
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source("../functions/bp_lineage.R")
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#########################################
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# Lineage and SNP count: lineage lf data
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#########################################
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# Relevel factors so that x-axis categ appear as you want
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lin_lf_plot = lin_lf
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lin_lf_plot
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is.factor(lin_lf_plot$sel_lineages_f)
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lin_lf_plot$sel_lineages_f = factor(lin_lf_plot$sel_lineages_f, c(""
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, "L1"
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, "L2"
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, "L3"
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, "L4"
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, "L5"
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, "L6"
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, "L7"
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, "LBOV"
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, "L1;L2"
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, "L1;L3"
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, "L1;L4"
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, "L2;L3"
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, "L2;L3;L4"
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, "L2;L4"
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, "L2;L6"
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, "L2;LBOV"
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, "L3;L4"
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, "L4;L6"
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, "L4;L7"))
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levels(lin_lf_plot$sel_lineages_f)
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lin_count_bp(lin_lf_plot
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, x_categ = "sel_lineages_f"
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, y_count = "p_count"
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, bar_fill_categ = "count_categ"
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, display_label_col = "p_count"
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, bar_stat_stype = "identity"
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, x_lab_angle = 90
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, my_xats = 20
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, bar_col_labels = c("Mutations", "Total Samples")
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, bar_col_values = c("grey50", "gray75")
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, y_log10 = T
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, y_label = "Count"
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, y_scale_percent = F)
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###############################################
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# Lineage SNP diversity count: lineage wf data
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###############################################
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# Relevel factors so that x-axis categ appear as you want
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lin_wf_plot = lin_wf
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is.factor(lin_wf_plot$sel_lineages_f)
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lin_wf_plot$sel_lineages_f = factor(lin_wf_plot$sel_lineages_f, c(""
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, "L1"
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, "L2"
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, "L3"
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, "L4"
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, "L5"
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, "L6"
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, "L7"
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, "LBOV"
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, "L1;L2"
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, "L1;L3"
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, "L1;L4"
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, "L2;L3"
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, "L2;L3;L4"
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, "L2;L4"
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, "L2;L6"
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, "L2;LBOV"
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, "L3;L4"
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, "L4;L6"
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, "L4;L7"))
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levels(lin_wf_plot$sel_lineages_f)
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#==========
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# Plot
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#==========
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lin_count_bp(lin_wf_plot
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, x_categ = "sel_lineages_f"
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, y_count = "snp_diversity"
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, display_label_col = "snp_diversity_f"
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, bar_stat_stype = "identity"
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, x_lab_angle = 90
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, my_xats = 20
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, y_scale_percent = T
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, y_label = "SNP diversity"
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)
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, x_categ = "sel_lineages_f"
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, y_count = "p_count"
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, bar_fill_categ = "count_categ"
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, display_label_col = "p_count"
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, bar_stat_stype = "identity"
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, x_lab_angle = 90
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, my_xats = 15
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, bar_col_labels = c("Mutations", "Total Samples")
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, bar_col_values = c("grey50", "gray75")
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, y_log10 = T
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, y_scale_percent = F
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@ -437,13 +437,19 @@ if (nrow(corr_ps_df3) == nrow(merged_df3) && nrow(merged_df3_comp) == check1) {
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, "\nGot: ", check1)
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}
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rm(foo)
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####################################################################
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# Data for DM OM Plots: Long format dfs
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####################################################################
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source("other_plots_data.R")
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####################################################################
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# Data for Lineage barplots: WF and LF dfs
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####################################################################
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source("lineage_bp_data.R")
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########################################################################
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# End of script
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########################################################################
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173
scripts/plotting/lineage_bp_data.R
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scripts/plotting/lineage_bp_data.R
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#!/usr/bin/env Rscript
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#########################################################
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# TASK: Script to format data for lineage barplots:
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# WF and LF data with lineage sample, and snp counts
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# sourced by get_plotting_dfs.R
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#########################################################
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# working dir and loading libraries
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# getwd()
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# setwd("~/git/LSHTM_analysis/scripts/plotting")
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# getwd()
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# make cmd
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# globals
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# drug = "streptomycin"
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# gene = "gid"
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# source("get_plotting_dfs.R")
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#=======================================================================
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#################################################
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# Get data with lineage count, and snp diversity
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#################################################
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table(merged_df2$lineage)
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if (table(merged_df2$lineage == "")[[2]]) {
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cat("\nMissing samples with lineage classification:", table(merged_df2$lineage == "")[[2]])
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}
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##################################
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# WF data: lineages with
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# snp count
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# total_samples
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# snp diversity (perc)
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##################################
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sel_lineages = levels(as.factor(merged_df2$lineage))
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lin_wf = data.frame(sel_lineages) #4, 1
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total_snps_u = NULL
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total_samples = NULL
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for (i in sel_lineages){
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#print(i)
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curr_total = length(unique(merged_df2$id)[merged_df2$lineage==i])
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#print(curr_total)
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total_samples = c(total_samples, curr_total)
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print(total_samples)
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foo = merged_df2[merged_df2$lineage==i,]
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print(paste0(i, "=======\n"))
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print(length(unique(foo$mutationinformation)))
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curr_count = length(unique(foo$mutationinformation))
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total_snps_u = c(total_snps_u, curr_count)
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}
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lin_wf
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# Add these counts as columns to the df
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lin_wf$num_snps_u = total_snps_u
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lin_wf$total_samples = total_samples
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# Add SNP diversity
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lin_wf$snp_diversity = lin_wf$num_snps_u/lin_wf$total_samples
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lin_wf
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#=====================
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# Add some formatting
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#=====================
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# SNP diversity
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lin_wf$snp_diversity_f = round( (lin_wf$snp_diversity * 100), digits = 0)
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lin_wf
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# Lineage names
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lin_wf$sel_lineages_f = gsub("lineage", "L", lin_wf$sel_lineages)
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lin_wf
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# # Lineage names
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# lin_wf = lin_wf %>%
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# mutate(ordering_category = case_when(
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# sel_lineages_f == "" ~ 0
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# , sel_lineages_f == "L1" ~ 1
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# , sel_lineages_f == "L2" ~ 2
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# , sel_lineages_f == "L3" ~ 3
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# , sel_lineages_f == "L4" ~ 4
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# , sel_lineages_f == "L5" ~ 5
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# , sel_lineages_f == "L6" ~ 6
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# , sel_lineages_f == "L7" ~ 7
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# , sel_lineages_f == "LBOV" ~ 8
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#
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# , sel_lineages_f == "L1;L2" ~ 9
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# , sel_lineages_f == "L1;L3" ~ 10
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# , sel_lineages_f == "L1;L4" ~ 11
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#
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# , sel_lineages_f == "L2;L3" ~ 12
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# , sel_lineages_f == "L2;L3;L4" ~ 13
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# , sel_lineages_f == "L2;L4" ~ 14
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# , sel_lineages_f == "L2;L6" ~ 15
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# , sel_lineages_f == "L2;LBOV" ~ 16
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#
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# , sel_lineages_f == "L3;L4" ~ 17
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#
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# , sel_lineages_f == "L4;L6" ~ 18
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# , sel_lineages_f == "L4;L7" ~ 19
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#
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# , FALSE ~ -1)
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# )
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##################################
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# LF data: lineages with
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# snp count
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# total_samples
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# snp diversity (perc)
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##################################
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names(lin_wf)
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tot_cols = ncol(lin_wf)
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pivot_cols = c("sel_lineages", "sel_lineages_f", "snp_diversity", "snp_diversity_f")
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pivot_cols_n = length(pivot_cols)
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expected_rows = nrow(lin_wf) * ( length(lin_wf) - pivot_cols_n )
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lin_lf <- gather(lin_wf
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, count_categ
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, p_count
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, num_snps_u:total_samples
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, factor_key = TRUE)
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lin_lf
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# quick checks
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if ( nrow(lin_lf) == expected_rows ){
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cat("\nPASS: Lineage LF data created"
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, "\nnrow: ", nrow(lin_lf)
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, "\nncol: ", ncol(lin_lf))
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} else {
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cat("\nFAIL: numbers mismatch"
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, "\nExpected nrow: ", expected_rows)
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}
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#######################################
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# #=====================
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# # Add some formatting
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# #=====================
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# lin_lf$sel_lineages_f = gsub("lineage", "L", lin_lf$sel_lineages)
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# lin_lf
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# lin_lf = lin_lf %>%
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# mutate(ordering_category = case_when(
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# sel_lineages_f == "" ~ 0
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# , sel_lineages_f == "L1" ~ 1
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# , sel_lineages_f == "L2" ~ 2
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# , sel_lineages_f == "L3" ~ 3
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# , sel_lineages_f == "L4" ~ 4
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# , sel_lineages_f == "L5" ~ 5
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# , sel_lineages_f == "L6" ~ 6
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# , sel_lineages_f == "L7" ~ 7
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# , sel_lineages_f == "LBOV" ~ 8
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#
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# , 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)
|
||||
# )
|
||||
|
|
@ -1,7 +1,8 @@
|
|||
#!/usr/bin/env Rscript
|
||||
#########################################################
|
||||
# TASK: producing boxplots for dr and other muts
|
||||
|
||||
# TASK: Script to format data for dm om plots:
|
||||
# generating LF data
|
||||
# sourced by get_plotting_dfs.R
|
||||
#########################################################
|
||||
# working dir and loading libraries
|
||||
# getwd()
|
||||
|
|
|
|||
Loading…
Add table
Add a link
Reference in a new issue