77 lines
3 KiB
R
77 lines
3 KiB
R
###############################
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# TASK: function to plot lineage
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# dist plots with or without facet
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# think about color palette
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# for stability
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##############################
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#n_colours = length(unique(lin_dist_plot$duet_scaled))
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#my_palette <- colorRampPalette(c(mcsm_red2, mcsm_red1, mcsm_mid, mcsm_blue1, mcsm_blue2))(n = n_colours+1)
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lineage_distP <- function(plotdf
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, x_axis = "duet_scaled"
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, y_axis = "lineage_labels"
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, x_lab = "DUET"
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, all_lineages = F
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, use_lineages = c("L1", "L2", "L3", "L4")
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, with_facet = F
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, facet_wrap_var = "" # FIXME: document what this is for
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, fill_categ = "mutation_info_labels"
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, fill_categ_cols = c("#E69F00", "#999999")
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, label_categories = c("R", "S")
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, my_ats = 15 # 15 axis text size
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, my_als = 20 # 20 axis label size
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, my_leg_ts = 16 #16
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, my_leg_title = 16 #16
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, my_strip_ts = 20 #20
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, leg_pos = c(0.8, 0.9)
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, leg_pos_wf = c("top", "left", "bottom", "right")
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, leg_dir_wf = c("horizontal", "vertical")
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, leg_label = "Mutation Group"
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, alpha = 0.7)
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{
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if(!all_lineages){
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plotdf = plotdf[plotdf[[y_axis]]%in%use_lineages,]
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}
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ggplot(plotdf, aes_string(x = x_axis
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, y = y_axis))+
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geom_density_ridges(aes_string(fill = fill_categ)
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, scale = 3
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, size = 0.3
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, alpha = alpha) +
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scale_x_continuous(expand = c(0.01, 0.01)) +
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#coord_cartesian( xlim = c(-1, 1)) +
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scale_fill_manual(values = fill_categ_cols
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, labels = label_categories) +
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theme(axis.text.x = element_text(size = my_ats
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, angle = 90
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, hjust = 1
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, vjust = 0.4)
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, axis.text.y = element_text(size = my_ats)
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, axis.title.x = element_text(size = my_ats)
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, axis.title.y = element_blank()
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, strip.text = element_text(size = my_strip_ts)
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, legend.text = element_text(size = my_leg_ts)
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, legend.key.size = unit(my_leg_ts, 'pt')
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, legend.title = element_text(size = my_leg_title)
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, legend.position = c(0.8, 0.9)) +
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labs(x = x_lab
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, fill = leg_label) +
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# FIXME: This didn't work BEFORE i fixed the ggplot() assignment thing!!!
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if (with_facet){
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# used reformulate or make as formula
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#fwv = reformulate(facet_wrap_var)
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fwv = as.formula(paste0("~", facet_wrap_var))
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facet_wrap(fwv) +
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theme(legend.position = leg_pos_wf
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, legend.direction = leg_dir_wf)
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}
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}
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