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playing with lineage_dist_dm_om

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This commit is contained in:
Tanushree Tunstall 2020-09-16 13:23:49 +01:00
parent 1bc7f83916
commit 19287f3b4b
2 changed files with 101 additions and 38 deletions
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6
scripts/plotting/or_plots_combined.R
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@ -132,6 +132,12 @@ p1 = g1 +
p1 p1
#=============
#ggplotly
# *so COOL*
fig <- ggplotly(p1)
fig
#==============
#------------------- #-------------------
# generate plot 2: Lig vs OR by position as geom_points # generate plot 2: Lig vs OR by position as geom_points
#------------------- #-------------------

133
scripts/plotting/scratch_plots/lineage_dist_combined_PS_style.R
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@ -53,11 +53,14 @@ cat("Variables imported:"
, "\nother_muts_col:", other_muts_col , "\nother_muts_col:", other_muts_col
, "\ndrtype_col:", resistance_col) , "\ndrtype_col:", resistance_col)
cat("cols imported:"
, mcsm_red2, mcsm_red1, mcsm_mid, mcsm_blue1, mcsm_blue2)
#======= #=======
# output # output
#======= #=======
#lineage_dist_dm_om = "lineage_dist_dm_om_PS.svg" lineage_dist_combined_dm_om = "lineage_dist_combined_dm_om_PS.svg"
#plot_lineage_dist_dm_om = paste0(plotdir,"/", lineage_dist_dm_om) plot_lineage_dist_combined_dm_om = paste0(plotdir,"/", lineage_dist_combined_dm_om)
#======================================================================== #========================================================================
########################### ###########################
@ -79,11 +82,6 @@ rm(my_df_u, merged_df2, merged_df2_comp, merged_df3, merged_df3_comp)
colnames(my_df) colnames(my_df)
str(my_df) str(my_df)
# Ensure correct data type in columns to plot: need to be factor
is.factor(my_df$lineage)
my_df$lineage = as.factor(my_df$lineage)
is.factor(my_df$lineage)
table(my_df$mutation_info) table(my_df$mutation_info)
#=================== #===================
@ -95,27 +93,34 @@ table(my_df$lineage); str(my_df$lineage)
sel_lineages = c("lineage1" sel_lineages = c("lineage1"
, "lineage2" , "lineage2"
, "lineage3" , "lineage3"
, "lineage4" , "lineage4")
#, "lineage5" #, "lineage5"
#, "lineage6" #, "lineage6"
#, "lineage7" #, "lineage7")
)
# works nicely with facet wrap using labeller, but not otherwise
#my_labels = c('Lineage 1'
# , 'Lineage 2'
# , 'Lineage 3'
# , 'Lineage 4')
# #, 'Lineage 5'
# #, 'Lineage 6'
# #, 'Lineage 7')
my_labels = c('Lineage 1', 'Lineage 2', 'Lineage 3', 'Lineage 4' #names(my_labels) = c('lineage1'
#, 'Lineage 5', 'Lineage 6', 'Lineage 7' # , 'lineage2'
) # , 'lineage3'
names(my_labels) = c('lineage1', 'lineage2', 'lineage3', 'lineage4' # , 'lineage4')
# , 'lineage5', 'lineage6', 'lineage7' # #, 'lineage5'
) # #, 'lineage6'
# #, 'lineage7')
#==========================
# subset selected lineages # subset selected lineages
df_lin = subset(my_df, subset = lineage %in% sel_lineages ) #==========================
df_lin = subset(my_df, subset = lineage %in% sel_lineages)
table(df_lin$lineage) table(df_lin$lineage)
# refactor
df_lin$lineage = factor(df_lin$lineage)
#{RESULT: Total number of samples for lineage} #{RESULT: Total number of samples for lineage}
sum(table(df_lin$lineage)) sum(table(df_lin$lineage))
@ -131,6 +136,30 @@ u = unique(df_lin$mutationinformation)
#{Result:Muts not present within selected lineages} #{Result:Muts not present within selected lineages}
check = u2[!u2%in%u]; print(check) check = u2[!u2%in%u]; print(check)
# workaround to make labels appear nicely for in otherwise cases
#==================
# lineage: labels
# from "plyr"
#==================
table(df_lin$lineage)
df_lin$lineage_labels = mapvalues(df_lin$lineage
, from = c("lineage1","lineage2", "lineage3", "lineage4")
, to = c("Lineage 1", "Lineage 2", "Lineage 3", "Lineage 4"))
table(df_lin$lineage_labels)
table(df_lin$lineage_labels) == table(df_lin$lineage)
#========================
# mutation_info: labels
#========================
table(df_lin$mutation_info)
df_lin$mutation_info_labels = ifelse(df_lin$mutation_info == dr_muts_col, "DM", "OM")
table(df_lin$mutation_info_labels)
table(df_lin$mutation_info) == table(df_lin$mutation_info_labels)
#======================= #=======================
# subset dr muts only # subset dr muts only
#======================= #=======================
@ -191,10 +220,10 @@ p1 = ggplot(df, aes(x = duet_scaled
#, jittered_points = TRUE #, jittered_points = TRUE
, scale = 3 , scale = 3
, size = 0.3 ) + , size = 0.3 ) +
facet_wrap( ~lineage facet_wrap( ~lineage_labels
, scales = "free" , scales = "free"
#, switch = 'x' #, labeller = labeller(lineage = my_labels)
, labeller = labeller(lineage = my_labels)) + ) +
coord_cartesian( xlim = c(-1, 1)) + coord_cartesian( xlim = c(-1, 1)) +
#scale_fill_gradientn(colours = c("#f8766d", "white", "#00bfc4") #scale_fill_gradientn(colours = c("#f8766d", "white", "#00bfc4")
# , name = "DUET" ) + # , name = "DUET" ) +
@ -212,8 +241,8 @@ p1 = ggplot(df, aes(x = duet_scaled
, axis.ticks.y = element_blank() , axis.ticks.y = element_blank()
, plot.title = element_blank() , plot.title = element_blank()
, strip.text = element_text(size = my_als) , strip.text = element_text(size = my_als)
, legend.text = element_text(size = my_als-5) , legend.text = element_text(size = my_als-6)
, legend.title = element_text(size = my_als) , legend.title = element_text(size = my_als-3)
) )
print(p1) print(p1)
@ -221,19 +250,18 @@ print(p1)
#======================================= #=======================================
# Plot 2: lineage dist by mutation_info # Plot 2: lineage dist by mutation_info
#======================================= #=======================================
mutation_info_labels = c("DM", "OM")
names(mutation_info_labels) = c(dr_muts_col, other_muts_col)
p3 = ggplot(df, aes(x = duet_scaled p2 = ggplot(df, aes(x = duet_scaled
, y = mutation_info))+ , y = mutation_info_labels))+
geom_density_ridges_gradient(aes(fill = ..x..) geom_density_ridges_gradient(aes(fill = ..x..)
#, jittered_points = TRUE #, jittered_points = TRUE
, scale = 3 , scale = 3
, size = 0.3 ) + , size = 0.3 ) +
facet_wrap(~lineage facet_wrap(~lineage_labels
# , scales = "free" #, scales = "free"
# #, switch = 'x' #, labeller = labeller(lineage = my_labels)
, labeller = labeller(lineage = my_labels, mutation_info = mutation_info_labels)) + ) +
coord_cartesian( xlim = c(-1, 1)) + coord_cartesian( xlim = c(-1, 1)) +
#scale_fill_gradientn(colours = c("#ae301e", "white", "#007d85") #scale_fill_gradientn(colours = c("#ae301e", "white", "#007d85")
# , name = "DUET" ) + # , name = "DUET" ) +
@ -245,29 +273,58 @@ p3 = ggplot(df, aes(x = duet_scaled
, hjust = 1 , hjust = 1
, vjust = 0.4) , vjust = 0.4)
#, axis.text.y = element_blank() , axis.text.y = element_text(size = my_ats)
, axis.title.x = element_blank() , axis.title.x = element_blank()
, axis.title.y = element_blank() , axis.title.y = element_blank()
, axis.ticks.y = element_blank() , axis.ticks.y = element_blank()
, plot.title = element_blank() , plot.title = element_blank()
, strip.text = element_text(size = my_als) , strip.text = element_text(size = my_als)
, legend.text = element_text(size = my_als-5) , legend.position = "none"
, legend.title = element_text(size = my_als) #, legend.text = element_text(size = my_als-5)
#, legend.title = element_text(size = my_als)
) )
print(p3) print(p2)
#============================== #==============================
p3 = ggplot(df, aes(x = duet_scaled
, y = lineage_labels))+
geom_density_ridges_gradient(aes(fill = factor(mutation_info_labels))
#, jittered_points = TRUE
, scale = 3
, size = 0.3 ) +
coord_cartesian( xlim = c(-1, 1)) +
scale_fill_manual(values = c("#E69F00", "#999999")) +
theme(axis.text.x = element_text(size = my_ats
, angle = 90
, hjust = 1
, vjust = 0.4)
, axis.text.y = element_text(size = my_ats)
, axis.title.x = element_text(size = my_ats)
, axis.title.y = element_blank()
, axis.ticks.y = element_blank()
, plot.title = element_blank()
, strip.text = element_text(size = my_als)
, legend.text = element_text(size = my_als-2)
, legend.title = element_text(size = my_als-3)
, legend.position = c(0.8, 0.9)) +
labs(x = "DUET", fill = "Mutation class")
# Modify legend titles
#p + labs(fill = "Dose (mg)")
p3
######################################################################## ########################################################################
#============== #==============
# combine plot # combine plot
#=============== #===============
svg(plot_lineage_dist_combined, width = 12, height = 6) svg(plot_lineage_dist_combined_dm_om, width = 12, height = 6)
printFile = cowplot::plot_grid(p1, p3 printFile = cowplot::plot_grid(p1, p3
, rel_widths = c(0.5/2, 0.5/2)
, label_size = my_als+10) , label_size = my_als+10)
print(printFile) print(printFile)