playing with lineage_dist_dm_om
This commit is contained in:
parent
ba02107e23
commit
25f2f9e4a2
2 changed files with 101 additions and 38 deletions
|
|
@ -132,6 +132,12 @@ p1 = g1 +
|
|||
|
||||
p1
|
||||
|
||||
#=============
|
||||
#ggplotly
|
||||
# *so COOL*
|
||||
fig <- ggplotly(p1)
|
||||
fig
|
||||
#==============
|
||||
#-------------------
|
||||
# generate plot 2: Lig vs OR by position as geom_points
|
||||
#-------------------
|
||||
|
|
|
|||
|
|
@ -53,11 +53,14 @@ cat("Variables imported:"
|
|||
, "\nother_muts_col:", other_muts_col
|
||||
, "\ndrtype_col:", resistance_col)
|
||||
|
||||
cat("cols imported:"
|
||||
, mcsm_red2, mcsm_red1, mcsm_mid, mcsm_blue1, mcsm_blue2)
|
||||
|
||||
#=======
|
||||
# output
|
||||
#=======
|
||||
#lineage_dist_dm_om = "lineage_dist_dm_om_PS.svg"
|
||||
#plot_lineage_dist_dm_om = paste0(plotdir,"/", lineage_dist_dm_om)
|
||||
lineage_dist_combined_dm_om = "lineage_dist_combined_dm_om_PS.svg"
|
||||
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)
|
||||
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$mutation_info)
|
||||
|
||||
#===================
|
||||
|
|
@ -95,27 +93,34 @@ table(my_df$lineage); str(my_df$lineage)
|
|||
sel_lineages = c("lineage1"
|
||||
, "lineage2"
|
||||
, "lineage3"
|
||||
, "lineage4"
|
||||
, "lineage4")
|
||||
#, "lineage5"
|
||||
#, "lineage6"
|
||||
#, "lineage7"
|
||||
)
|
||||
#, "lineage7")
|
||||
|
||||
# works nicely with facet wrap using labeller, but not otherwise
|
||||
#my_labels = c('Lineage 1'
|
||||
# , 'Lineage 2'
|
||||
# , 'Lineage 3'
|
||||
# , 'Lineage 4')
|
||||
# #, 'Lineage 5'
|
||||
# #, 'Lineage 6'
|
||||
# #, 'Lineage 7')
|
||||
|
||||
my_labels = c('Lineage 1', 'Lineage 2', 'Lineage 3', 'Lineage 4'
|
||||
#, 'Lineage 5', 'Lineage 6', 'Lineage 7'
|
||||
)
|
||||
names(my_labels) = c('lineage1', 'lineage2', 'lineage3', 'lineage4'
|
||||
# , 'lineage5', 'lineage6', 'lineage7'
|
||||
)
|
||||
#names(my_labels) = c('lineage1'
|
||||
# , 'lineage2'
|
||||
# , 'lineage3'
|
||||
# , 'lineage4')
|
||||
# #, 'lineage5'
|
||||
# #, 'lineage6'
|
||||
# #, 'lineage7')
|
||||
|
||||
#==========================
|
||||
# subset selected lineages
|
||||
df_lin = subset(my_df, subset = lineage %in% sel_lineages )
|
||||
#==========================
|
||||
df_lin = subset(my_df, subset = lineage %in% sel_lineages)
|
||||
table(df_lin$lineage)
|
||||
|
||||
# refactor
|
||||
df_lin$lineage = factor(df_lin$lineage)
|
||||
|
||||
#{RESULT: Total number of samples for lineage}
|
||||
sum(table(df_lin$lineage))
|
||||
|
||||
|
|
@ -131,6 +136,30 @@ u = unique(df_lin$mutationinformation)
|
|||
#{Result:Muts not present within selected lineages}
|
||||
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
|
||||
#=======================
|
||||
|
|
@ -191,10 +220,10 @@ p1 = ggplot(df, aes(x = duet_scaled
|
|||
#, jittered_points = TRUE
|
||||
, scale = 3
|
||||
, size = 0.3 ) +
|
||||
facet_wrap( ~lineage
|
||||
facet_wrap( ~lineage_labels
|
||||
, scales = "free"
|
||||
#, switch = 'x'
|
||||
, labeller = labeller(lineage = my_labels)) +
|
||||
#, labeller = labeller(lineage = my_labels)
|
||||
) +
|
||||
coord_cartesian( xlim = c(-1, 1)) +
|
||||
#scale_fill_gradientn(colours = c("#f8766d", "white", "#00bfc4")
|
||||
# , name = "DUET" ) +
|
||||
|
|
@ -212,8 +241,8 @@ p1 = ggplot(df, aes(x = duet_scaled
|
|||
, axis.ticks.y = element_blank()
|
||||
, plot.title = element_blank()
|
||||
, strip.text = element_text(size = my_als)
|
||||
, legend.text = element_text(size = my_als-5)
|
||||
, legend.title = element_text(size = my_als)
|
||||
, legend.text = element_text(size = my_als-6)
|
||||
, legend.title = element_text(size = my_als-3)
|
||||
)
|
||||
|
||||
print(p1)
|
||||
|
|
@ -221,19 +250,18 @@ print(p1)
|
|||
#=======================================
|
||||
# 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
|
||||
, y = mutation_info))+
|
||||
p2 = ggplot(df, aes(x = duet_scaled
|
||||
, y = mutation_info_labels))+
|
||||
geom_density_ridges_gradient(aes(fill = ..x..)
|
||||
#, jittered_points = TRUE
|
||||
, scale = 3
|
||||
, size = 0.3 ) +
|
||||
facet_wrap(~lineage
|
||||
# , scales = "free"
|
||||
# #, switch = 'x'
|
||||
, labeller = labeller(lineage = my_labels, mutation_info = mutation_info_labels)) +
|
||||
facet_wrap(~lineage_labels
|
||||
#, scales = "free"
|
||||
#, labeller = labeller(lineage = my_labels)
|
||||
) +
|
||||
|
||||
coord_cartesian( xlim = c(-1, 1)) +
|
||||
#scale_fill_gradientn(colours = c("#ae301e", "white", "#007d85")
|
||||
# , name = "DUET" ) +
|
||||
|
|
@ -245,29 +273,58 @@ p3 = ggplot(df, aes(x = duet_scaled
|
|||
, hjust = 1
|
||||
, vjust = 0.4)
|
||||
|
||||
#, axis.text.y = element_blank()
|
||||
, axis.text.y = element_text(size = my_ats)
|
||||
, axis.title.x = element_blank()
|
||||
, 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-5)
|
||||
, legend.title = element_text(size = my_als)
|
||||
, legend.position = "none"
|
||||
#, 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
|
||||
#===============
|
||||
|
||||
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
|
||||
, rel_widths = c(0.5/2, 0.5/2)
|
||||
, label_size = my_als+10)
|
||||
|
||||
print(printFile)
|
||||
|
|
|
|||
Loading…
Add table
Add a link
Reference in a new issue