renamed file in scratch plot/
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1 changed files with 112 additions and 83 deletions
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@ -179,14 +179,9 @@ table(my_df_other$lineage)
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########################################################################
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########################################################################
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#==========================
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#==========================
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# Plot 1: ALL Muts
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# Distribution plots
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# x = mcsm_values, y = dist
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# fill = stability
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#============================
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#============================
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#my_plot_name_dm_om = 'lineage_dist_DM_OM_PS.svg'
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#plot_lineage_dm_om_duet = paste0(plotdir,"/", my_plot_name_dm_om)
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#%%%%%%%%%%%%%%%%%%%%%%%%%
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#%%%%%%%%%%%%%%%%%%%%%%%%%
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# REASSIGNMENT
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# REASSIGNMENT
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df <- df_lin
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df <- df_lin
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@ -200,73 +195,29 @@ rm(df_lin)
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# 2 : ggridges (good!)
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# 2 : ggridges (good!)
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my_ats = 15 # axis text size
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my_ats = 15 # axis text size
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my_als = 20 # axis label size
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my_als = 20 # axis label size
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#=======================
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# Plot 1: lineage dist
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#=======================
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# check plot name
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plot_lineage_duet
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n_colours = length(unique(df$duet_scaled))
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n_colours = length(unique(df$duet_scaled))
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#my_palette <- colorRampPalette(c(mcsm_red, "#f8766d", "white","#00bfc4", mcsm_blue))(n = 400)
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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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my_palette <- colorRampPalette(c(mcsm_red2, mcsm_red1, mcsm_mid, mcsm_blue1, mcsm_blue2))(n = n_colours+1)
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# output svg
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#=======================================
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#svg(plot_lineage_duet)
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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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# 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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p1 = ggplot(df, aes(x = duet_scaled
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p1 = ggplot(df, aes(x = duet_scaled
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, y = duet_outcome))+
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, y = lineage_labels))+
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geom_density_ridges_gradient(aes(fill = ..x..)
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geom_density_ridges_gradient(aes(fill = ..x..)
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#, jittered_points = TRUE
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#, jittered_points = TRUE
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, scale = 3
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, scale = 3
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, size = 0.3 ) +
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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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coord_cartesian( xlim = c(-1, 1)) +
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#scale_fill_gradientn(colours = c("#f8766d", "white", "#00bfc4")
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# , name = "DUET" ) +
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#scale_fill_gradientn(colours = c(mcsm_red, "#f8766d", "white","#00bfc4", mcsm_blue)
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# , name = "DUET" ) +
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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_blank()
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, axis.title.x = element_blank()
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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-6)
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, legend.title = element_text(size = my_als-3)
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)
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print(p1)
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#dev.off()
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#=======================================
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# Plot 2: lineage dist by mutation_info
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#=======================================
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p2 = ggplot(df, aes(x = duet_scaled
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, y = mutation_info_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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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 = c("#ae301e", "white", "#007d85")
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# , name = "DUET" ) +
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#scale_fill_gradientn(colours = c("mcsm_red", "white", "mcsm_blue")
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# , name = "DUET" ) +
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scale_fill_gradientn(colours = my_palette, name = "DUET") +
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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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theme(axis.text.x = element_text(size = my_ats
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, angle = 90
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, angle = 90
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@ -274,26 +225,42 @@ p2 = ggplot(df, aes(x = duet_scaled
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, vjust = 0.4)
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, vjust = 0.4)
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, axis.text.y = element_text(size = my_ats)
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, axis.text.y = element_text(size = my_ats)
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, axis.title.x = element_blank()
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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.title.y = element_blank()
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, axis.ticks.y = element_blank()
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, axis.ticks.y = element_blank()
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, plot.title = 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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, strip.text = element_text(size = my_als)
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, legend.position = "none"
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, legend.text = element_text(size = my_als-10)
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#, legend.text = element_text(size = my_als-5)
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, legend.title = element_text(size = my_als-3)
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#, legend.title = element_text(size = my_als)
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, legend.position = c(0.8, 0.8)) +
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)
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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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print(p2)
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p1
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#==============================
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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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p3 = ggplot(df, aes(x = duet_scaled
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#p1_copy
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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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# y = lineage_labels
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# fill = mutation_info
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# NO FACET
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#=======================================
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# output svg
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#plot_lineage_dist_duet_dm_om = paste0(plotdir,"/", "lineage_dist_duet_dm_om.svg")
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#plot_lineage_dist_duet_dm_om
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#svg(plot_lineage_dist_duet_dm_om)
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p2 = ggplot(df, aes(x = duet_scaled
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, y = lineage_labels))+
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, y = lineage_labels))+
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geom_density_ridges_gradient(aes(fill = factor(mutation_info_labels))
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geom_density_ridges(aes(fill = factor(mutation_info_labels))
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#, jittered_points = TRUE
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, scale = 3
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, scale = 3
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, size = 0.3
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, size = 0.3 ) +
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, alpha = 0.8) +
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coord_cartesian( xlim = c(-1, 1)) +
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coord_cartesian( xlim = c(-1, 1)) +
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scale_fill_manual(values = c("#E69F00", "#999999")) +
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scale_fill_manual(values = c("#E69F00", "#999999")) +
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theme(axis.text.x = element_text(size = my_ats
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theme(axis.text.x = element_text(size = my_ats
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@ -309,23 +276,85 @@ p3 = ggplot(df, aes(x = duet_scaled
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, legend.text = element_text(size = my_als-2)
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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.title = element_text(size = my_als-3)
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, legend.position = c(0.8, 0.9)) +
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, legend.position = c(0.8, 0.9)) +
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labs(x = "DUET", fill = "Mutation class")
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labs(x = "DUET"
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, fill = "Mutation class") # legend title
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# Modify legend titles
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p2
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#p + labs(fill = "Dose (mg)")
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p3
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########################################################################
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########################################################################
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#==============
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#==============
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# combine plot
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# combine plot
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#===============
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#===============
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plot_lineage_dist_combined_dm_om
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svg(plot_lineage_dist_combined_dm_om, width = 12, height = 6)
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svg(plot_lineage_dist_combined_dm_om, width = 12, height = 6)
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printFile = cowplot::plot_grid(p1, p3
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printFile = cowplot::plot_grid(p1, p2
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, rel_widths = c(0.5/2, 0.5/2)
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, rel_widths = c(0.5/2, 0.5/2)
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, label_size = my_als+10)
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, label_size = my_als+10)
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print(printFile)
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print(printFile)
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dev.off()
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dev.off()
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########################################################################
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# alternate combination
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########################################################################
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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 = duet_outcome
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# FACET (f) = lineage
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#=======================
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# output individual svg
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#plot_lineage_dist_duet = paste0(plotdir,"/", "lineage_dist_duet_f.svg")
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#plot_lineage_dist_duet
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#svg(plot_lineage_dist_duet)
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p3 = ggplot(df, aes(x = duet_scaled
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, y = duet_outcome))+
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geom_density_ridges_gradient(aes(fill = ..x..)
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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) # sorted by lineage_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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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.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-6)
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, legend.title = element_text(size = my_als-3))+
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labs(x = "DUET")
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print(p3)
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#dev.off()
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#==============
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# combine plot: alt version
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#===============
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plot_lineage_dist_duet_fandnf = paste0(plotdir,"/", "lineage_dist_duet_fandnf.svg")
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plot_lineage_dist_duet_fandnf
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svg(plot_lineage_dist_duet_fandnf, width = 12, height = 6)
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printFile = cowplot::plot_grid(p3, p2
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, rel_widths = c(0.5/2, 0.5/2)
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, label_size = my_als+10)
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print(printFile)
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dev.off()
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