lf_bp2
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4 changed files with 193 additions and 12 deletions
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@ -28,7 +28,8 @@ lf_bp <- function(lf_df = lf_duet
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, stat_grp_comp = c("R", "S")
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, stat_method = "wilcox.test"
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, my_paired = FALSE
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, stat_label = c("p.format", "p.signif") ){
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, stat_label = c("p.format", "p.signif")
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) {
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fwv = as.formula(paste0("~", facet_var))
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#fwv = reformulate(facet_var)
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@ -57,13 +58,22 @@ lf_bp <- function(lf_df = lf_duet
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, outlier.colour = NA
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#, position = position_dodge(width = 0.9)
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, width = bp_width) +
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geom_quasirandom(priority = "density"
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geom_quasirandom(#priority = "density"
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#, shape = 21
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, size = dot_size
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size = dot_size
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, alpha = dot_transparency
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, show.legend = FALSE
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, cex = 0.8
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, aes(colour = factor(eval(parse(text = colour_categ))) ))
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, aes(
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colour = factor(
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eval(
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parse(
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text = colour_categ
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)
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)
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)
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)
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) + ggplot2::scale_color_manual(values = consurf_bp_colours)
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} else {
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#Legend=factor(eval(parse(text = colour_categ)))
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@ -71,16 +81,26 @@ lf_bp <- function(lf_df = lf_duet
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p2 = p1 +
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#theme(legend.title=element_text('XXX')) + # Legend doesn't need a title)
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geom_quasirandom(priority = "density"
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geom_quasirandom(#priority = "density"
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#, shape = 21
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, size = dot_size
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size = dot_size
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, alpha = dot_transparency
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, show.legend = FALSE
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# , fast = FALSE
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, cex = 0.8
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, aes(colour = factor(eval(parse(text = colour_categ))) )
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, aes(
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colour = factor(
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eval(
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parse(
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text = colour_categ
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)
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)
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)
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)
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#, aes(colour = Legend)
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)
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) +
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ggplot2::scale_color_manual(values = consurf_bp_colours)
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}
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@ -115,6 +135,7 @@ lf_bp <- function(lf_df = lf_duet
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, method = stat_method
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, paired = my_paired
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, label = stat_label[2])
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return(OutPlot)
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}
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147
scripts/functions/lf_bp2.R
Normal file
147
scripts/functions/lf_bp2.R
Normal file
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@ -0,0 +1,147 @@
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#############################
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# Barplots: ggplot
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# stats +/-
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# violin +/-
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# barplot +/
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# beeswarm
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#############################
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lf_bp2 <- function(lf_df = lf_duet
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, p_title = "DUET-DDG"
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, colour_categ = "outcome"
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, x_grp = "mutation_info_labels"
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, y_var = "param_value"
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, facet_var = "param_type"
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, n_facet_row = 1
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, y_scales = "free_y"
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, colour_bp_strip = "khaki2"
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, dot_size = 3
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, dot_transparency = 0.5
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, violin_quantiles = c(0.25, 0.5, 0.75) # can be NULL
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, my_ats = 22 # axis text size
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, my_als = 20 # axis label size
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, my_fls = 20 # facet label size
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, my_pts = 22 # plot title size)
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, make_boxplot = FALSE
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#, bp_width = c("auto", 0.5)
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, bp_width = "auto"
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, add_stats = TRUE
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, stat_grp_comp = c("R", "S")
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, stat_method = "wilcox.test"
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, my_paired = FALSE
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, stat_label = c("p.format", "p.signif")
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, monochrome = FALSE
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) {
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fwv = as.formula(paste0("~", facet_var))
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#fwv = reformulate(facet_var)
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# Only use the longer colour palette if there are many outcomes
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if (length(levels(lf_df$outcome)) > 2) {
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lf_bp_colours = consurf_bp_colours
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}
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else {
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lf_bp_colours =NULL
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#lf_bp_colours = hue_pal()(2)
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}
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if (bp_width == "auto"){
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bp_width = 0.5/length(unique(lf_df[[x_grp]]))
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}else{
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bp_width = bp_width
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}
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ggplot(lf_df, aes_string(x = x_grp, y = y_var)) +
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facet_wrap(fwv
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, nrow = n_facet_row
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, scales = y_scales) +
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ggplot2::scale_color_manual(values = lf_bp_colours) +
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geom_violin(trim = T
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, scale = "width"
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#, position = position_dodge(width = 0.9)
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, draw_quantiles = violin_quantiles) +
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# Add formatting to graph
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theme(axis.text.x = element_text(size = my_ats)
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, axis.text.y = element_text(size = my_ats
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, angle = 0
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, hjust = 1
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, vjust = 0)
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, axis.title.x = element_text(size = my_ats)
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, axis.title.y = element_text(size = my_ats)
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, plot.title = element_text(size = my_pts
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, hjust = 0.5
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, colour = "black"
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, face = "bold")
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, strip.background = element_rect(fill = colour_bp_strip)
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, strip.text.x = element_text(size = my_fls
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, colour = "black")
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, legend.title = element_text(color = "black"
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, size = my_als)
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, legend.text = element_text(size = my_ats)
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, legend.direction = "vertical") +
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labs(title = p_title
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, x = ""
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, y = "") +
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if (add_stats){
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my_comparisonsL <- list( stat_grp_comp )
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stat_compare_means(comparisons = my_comparisonsL
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, method = stat_method
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, paired = my_paired
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, label = stat_label[2])
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if (make_boxplot){
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geom_boxplot(fill = "white"
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, outlier.colour = NA
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#, position = position_dodge(width = 0.9)
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, width = bp_width) +
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geom_quasirandom(#priority = "density"
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#, shape = 21
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size = dot_size
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, alpha = dot_transparency
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, show.legend = FALSE
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, cex = 0.8
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, aes(
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colour = factor(
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eval(
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parse(
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text = colour_categ
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)
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)
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)
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)
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)
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} else {
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geom_quasirandom(
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size = dot_size
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, alpha = dot_transparency
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, show.legend = FALSE
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# , fast = FALSE
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, cex = 0.8
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, aes(
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colour = factor(
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eval(
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parse(
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text = colour_categ
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)
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)
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)
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)
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)
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}
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}
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}
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#lf_bp2(lf_consurf)
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@ -110,15 +110,15 @@ LogoPlotCustomH <- function(plot_df
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}
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class(logo_dfP_wf)
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#class(logo_dfP_wf)
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rownames(logo_dfP_wf) = logo_dfP_wf[,1]
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dim(logo_dfP_wf)
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#dim(logo_dfP_wf)
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logo_dfP_wf = logo_dfP_wf[,-1]
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str(logo_dfP_wf)
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#str(logo_dfP_wf)
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colnames(logo_dfP_wf)
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#colnames(logo_dfP_wf)
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position_or = as.numeric(colnames(logo_dfP_wf))
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######################################
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