added new layput for dm_om and facet_lineage plot
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1 changed files with 90 additions and 22 deletions
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@ -146,6 +146,7 @@ check = u2[!u2%in%u]; print(check)
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# lineage: labels
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# from "plyr"
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#==================
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#{Result:No of samples in selected lineages}
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table(df_lin$lineage)
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df_lin$lineage_labels = mapvalues(df_lin$lineage
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@ -166,6 +167,19 @@ table(df_lin$mutation_info_labels)
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table(df_lin$mutation_info) == table(df_lin$mutation_info_labels)
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#========================
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# duet_outcome: labels
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#========================
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#{Result: No. of D and S mutations in selected lineages}
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table(df_lin$duet_outcome)
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df_lin$duet_outcome_labels = ifelse(df_lin$duet_outcome == "Destabilising", "D", "S")
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table(df_lin$duet_outcome_labels)
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table(df_lin$duet_outcome) == table(df_lin$duet_outcome_labels)
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#=======================
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# subset dr muts only
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#=======================
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@ -208,28 +222,37 @@ my_palette <- colorRampPalette(c(mcsm_red2, mcsm_red1, mcsm_mid, mcsm_blue1, mcs
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# Plot 1: lineage dist: geom_density_ridges_gradient (allows aesthetics to vary along ridgeline, no alpha setting!)
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# else same as geom_density_ridges)
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# x = duet_scaled
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# y = lineage_labels
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# y = duet_outcome
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# fill = duet_scaled
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# NO FACET (nf)
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# Facet: Lineage
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#=======================================
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# output individual svg
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#plot_lineage_dist_duet_nf = paste0(plotdir,"/", "lineage_dist_duet_nf.svg")
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#plot_lineage_dist_duet_nf
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#svg(plot_lineage_dist_duet_nf)
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#plot_lineage_dist_duet_f paste0(plotdir,"/", "lineage_dist_duet_f.svg")
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#plot_lineage_dist_duet_f
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#svg(plot_lineage_dist_duet_f)
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p1 = ggplot(df, aes(x = duet_scaled
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, y = lineage_labels))+
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, y = duet_outcome))+
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geom_density_ridges_gradient(aes(fill = ..x..)
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#, jittered_points = TRUE
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, scale = 3
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, size = 0.3 ) +
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facet_wrap( ~lineage_labels
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# , scales = "free"
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# , labeller = labeller(lineage = my_labels)
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) +
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coord_cartesian( xlim = c(-1, 1)) +
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scale_fill_gradientn(colours = my_palette, name = "DUET") +
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scale_fill_gradientn(colours = my_palette
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, name = "DUET"
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#, breaks = c(-1, 0, 1)
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#, labels = c(-1,0,1)
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#, limits = c(-1,1)
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) +
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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_blank()
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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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@ -237,18 +260,19 @@ p1 = ggplot(df, aes(x = duet_scaled
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, plot.title = element_blank()
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, strip.text = element_text(size = my_als)
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, legend.text = element_text(size = my_als-10)
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, legend.title = element_text(size = my_als-3)
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, legend.position = c(0.8, 0.8)) +
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#, legend.direction = "horizontal")+
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#, legend.position = "top", )+
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#, legend.title = element_text(size = my_als-6)
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, legend.title = element_blank()
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, legend.position = c(-0.08, 0.41)
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#, legend.direction = "horizontal"
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#, legend.position = "left"
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)+
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labs(x = "DUET")
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p1
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#p1_copy = p1 + guides(fill = guide_colourbar(label = FALSE))
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#p1_copy= p1_copy + guides(size=guide_legend("Source", override.aes=list(shape=15, size = 10)))
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#p1_copy
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#p1_with_legend = p1 + guides(fill = guide_colourbar(label = FALSE))
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#=======================================
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# Plot 2: lineage dist: geom_density_ridges, allows alpha to be set
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# x = duet_scaled
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@ -279,14 +303,55 @@ p2 = ggplot(df, aes(x = duet_scaled
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, axis.ticks.y = element_blank()
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, plot.title = element_blank()
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, strip.text = element_text(size = my_als)
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, legend.text = element_text(size = my_als-2)
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, legend.title = element_text(size = my_als-3)
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, legend.text = element_text(size = my_als-4)
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, legend.title = element_text(size = my_als-4)
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, legend.position = c(0.8, 0.9)) +
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labs(x = "DUET"
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, fill = "Mutation class") # legend title
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p2
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#=======================================
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# Plot 3: lineage dist: geom_density_ridges_gradient (allows aesthetics to vary along ridgeline, no alpha setting!)
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# else same as geom_density_ridges)
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# x = duet_scaled
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# y = lineage_labels
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# fill = duet_scaled
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# NO FACET (nf)
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#=======================================
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# output individual svg
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#plot_lineage_dist_duet_nf = paste0(plotdir,"/", "lineage_dist_duet_nf.svg")
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#plot_lineage_dist_duet_nf
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#svg(plot_lineage_dist_duet_nf)
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p3 = ggplot(df, aes(x = duet_scaled
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, y = lineage_labels))+
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geom_density_ridges_gradient(aes(fill = ..x..)
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#, jittered_points = TRUE
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, scale = 3
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, size = 0.3 ) +
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coord_cartesian( xlim = c(-1, 1)) +
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scale_fill_gradientn(colours = my_palette, name = "DUET") +
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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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, axis.ticks.y = element_blank()
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, plot.title = element_blank()
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, strip.text = element_text(size = my_als)
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, legend.text = element_text(size = my_als-10)
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, legend.title = element_text(size = my_als-3)
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, legend.position = c(0.8, 0.8)) +
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#, legend.direction = "horizontal")+
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#, legend.position = "top")+
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labs(x = "DUET")
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p3
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########################################################################
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#==============
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# combine plots
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@ -308,6 +373,9 @@ svg(plot_lineage_dist_combined_dm_om_L, width = 12, height = 6)
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OutPlot2 = cowplot::plot_grid(p1, p2
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, labels = c("(a)", "(b)")
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#, label_x = -0.045, label_y = 0.92
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#, hjust = -0.7, vjust = -0.5
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#, align = "h"
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, rel_widths = c(0.5/2, 0.5/2)
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, label_size = my_als)
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