playing with lineage_dist_dm_om
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2 changed files with 101 additions and 38 deletions
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@ -132,6 +132,12 @@ p1 = g1 +
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p1
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#=============
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#ggplotly
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# *so COOL*
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fig <- ggplotly(p1)
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fig
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#==============
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#-------------------
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# generate plot 2: Lig vs OR by position as geom_points
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#-------------------
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@ -53,11 +53,14 @@ cat("Variables imported:"
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, "\nother_muts_col:", other_muts_col
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, "\ndrtype_col:", resistance_col)
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cat("cols imported:"
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, mcsm_red2, mcsm_red1, mcsm_mid, mcsm_blue1, mcsm_blue2)
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#=======
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# output
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#=======
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#lineage_dist_dm_om = "lineage_dist_dm_om_PS.svg"
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#plot_lineage_dist_dm_om = paste0(plotdir,"/", lineage_dist_dm_om)
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lineage_dist_combined_dm_om = "lineage_dist_combined_dm_om_PS.svg"
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plot_lineage_dist_combined_dm_om = paste0(plotdir,"/", lineage_dist_combined_dm_om)
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#========================================================================
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###########################
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@ -79,11 +82,6 @@ rm(my_df_u, merged_df2, merged_df2_comp, merged_df3, merged_df3_comp)
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colnames(my_df)
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str(my_df)
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# Ensure correct data type in columns to plot: need to be factor
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is.factor(my_df$lineage)
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my_df$lineage = as.factor(my_df$lineage)
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is.factor(my_df$lineage)
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table(my_df$mutation_info)
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#===================
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@ -95,27 +93,34 @@ table(my_df$lineage); str(my_df$lineage)
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sel_lineages = c("lineage1"
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, "lineage2"
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, "lineage3"
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, "lineage4"
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, "lineage4")
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#, "lineage5"
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#, "lineage6"
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#, "lineage7"
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)
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#, "lineage7")
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# works nicely with facet wrap using labeller, but not otherwise
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#my_labels = c('Lineage 1'
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# , 'Lineage 2'
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# , 'Lineage 3'
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# , 'Lineage 4')
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# #, 'Lineage 5'
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# #, 'Lineage 6'
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# #, 'Lineage 7')
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my_labels = c('Lineage 1', 'Lineage 2', 'Lineage 3', 'Lineage 4'
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#, 'Lineage 5', 'Lineage 6', 'Lineage 7'
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)
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names(my_labels) = c('lineage1', 'lineage2', 'lineage3', 'lineage4'
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# , 'lineage5', 'lineage6', 'lineage7'
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)
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#names(my_labels) = c('lineage1'
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# , 'lineage2'
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# , 'lineage3'
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# , 'lineage4')
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# #, 'lineage5'
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# #, 'lineage6'
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# #, 'lineage7')
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#==========================
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# subset selected lineages
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df_lin = subset(my_df, subset = lineage %in% sel_lineages )
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#==========================
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df_lin = subset(my_df, subset = lineage %in% sel_lineages)
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table(df_lin$lineage)
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# refactor
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df_lin$lineage = factor(df_lin$lineage)
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#{RESULT: Total number of samples for lineage}
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sum(table(df_lin$lineage))
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@ -131,6 +136,30 @@ u = unique(df_lin$mutationinformation)
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#{Result:Muts not present within selected lineages}
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check = u2[!u2%in%u]; print(check)
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# workaround to make labels appear nicely for in otherwise cases
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#==================
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# lineage: labels
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# from "plyr"
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#==================
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table(df_lin$lineage)
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df_lin$lineage_labels = mapvalues(df_lin$lineage
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, from = c("lineage1","lineage2", "lineage3", "lineage4")
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, to = c("Lineage 1", "Lineage 2", "Lineage 3", "Lineage 4"))
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table(df_lin$lineage_labels)
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table(df_lin$lineage_labels) == table(df_lin$lineage)
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#========================
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# mutation_info: labels
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#========================
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table(df_lin$mutation_info)
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df_lin$mutation_info_labels = ifelse(df_lin$mutation_info == dr_muts_col, "DM", "OM")
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table(df_lin$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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# subset dr muts only
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#=======================
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@ -191,10 +220,10 @@ p1 = ggplot(df, aes(x = duet_scaled
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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
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facet_wrap( ~lineage_labels
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, scales = "free"
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#, switch = 'x'
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, labeller = labeller(lineage = my_labels)) +
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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("#f8766d", "white", "#00bfc4")
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# , name = "DUET" ) +
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@ -212,8 +241,8 @@ p1 = 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-5)
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, legend.title = 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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@ -221,19 +250,18 @@ print(p1)
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#=======================================
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# Plot 2: lineage dist by mutation_info
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#=======================================
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mutation_info_labels = c("DM", "OM")
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names(mutation_info_labels) = c(dr_muts_col, other_muts_col)
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p3 = ggplot(df, aes(x = duet_scaled
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, y = mutation_info))+
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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
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# , scales = "free"
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# #, switch = 'x'
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, labeller = labeller(lineage = my_labels, mutation_info = mutation_info_labels)) +
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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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@ -245,29 +273,58 @@ p3 = ggplot(df, aes(x = duet_scaled
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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_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-5)
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, legend.title = element_text(size = my_als)
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, legend.position = "none"
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#, legend.text = element_text(size = my_als-5)
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#, legend.title = element_text(size = my_als)
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)
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print(p3)
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print(p2)
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#==============================
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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 = factor(mutation_info_labels))
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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_manual(values = c("#E69F00", "#999999")) +
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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-2)
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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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labs(x = "DUET", fill = "Mutation class")
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# Modify legend titles
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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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# combine plot
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#===============
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svg(plot_lineage_dist_combined, 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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, 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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