added ggridges_lineage_country.R for dist by country

scripts/plotting/ggridges_lineage_country.R

@@ -0,0 +1,279 @@
+
+
+#########################################################
+# 1: Installing and loading required packages
+#########################################################
+
+#source("../Header_TT.R")
+install.packages("qqman")
+library(qqman)
+
+source("combining_dfs_plotting.R")
+#mcsm_data: raw file, 225, 15
+#merged_df2 = 2201, 35
+#merged_df3 =  205, 35 ("Can't trust non-numerical params')
+
+#===============================================
+# PLOTS: DUET vs GWAS: non-numerical
+# lineage, country_code, etc
+# merged_df2: 1592, 35
+#===============================================
+
+#########################
+# Data for plot
+#########################
+df = merged_df2
+df = merged_df2_comp 
+
+
+#========================
+# Plot 1a: Lineage barplot
+# x = lineage y = No of samples
+# col = Lineage
+# fill = lineage
+#========================
+is.factor(df$lineage)
+df$lineage = as.factor(df$lineage)
+is.factor(df$lineage)
+
+table(df$lineage)
+
+# subset only lineages1-4
+sel_lineages = c("lineage1"
+                 , "lineage2"
+                 , "lineage3"
+                 , "lineage4"
+                 #, "lineage5"
+                 #, "lineage6"
+                 #, "lineage7"
+)
+
+# uncomment as necessary
+df_lin = subset(df, subset = lineage %in% sel_lineages )
+table(df_lin$lineage)
+
+#%%%%%%%%%%%%%%%%%%%%%%%%%
+# REASSIGNMENT
+df <- df_lin
+#%%%%%%%%%%%%%%%%%%%%%%%%%
+
+############## begin plot
+g = ggplot(df, aes(x = lineage))
+g + geom_bar(aes(fill = lineage)) +
+  theme( axis.text.x = element_text(size = 13
+                                    , angle = 90
+                                    , hjust = 1
+                                    , vjust = 0.4)
+         , axis.text.y = element_text(size = 15
+                                      , angle = 0
+                                      , hjust = 1
+                                      , vjust = 0)
+         , axis.title.x = element_text(size = 15)
+         , axis.title.y = element_text(size = 15) ) +
+  labs(title = "Lineage"
+       , x = "Lineage"
+       , y = "No of samples")
+
+
+#========================
+# Plot 2: DUET, lineage, country_code and or_mychisq
+# x = lineage y = DUET
+# col = Lineage
+# fill = country_code
+#========================
+### begin plot
+g = ggplot(df, aes(x = country_code
+                   , y = duet_scaled))
+g + geom_point(aes(col = lineage
+                   , size = or_mychisq)) +
+  theme(axis.text.x = element_text(size = 13
+                                    , angle = 90
+                                    , hjust = 1
+                                    , vjust = 0.4)
+         , axis.text.y = element_text(size = 15
+                                      , angle = 0
+                                      , hjust = 1
+                                      , vjust = 0)
+         , axis.title.x = element_text(size = 15)
+         , axis.title.y = element_text(size = 15) ) +
+  labs(title = "DUET, country_code, lineage, or_mychisq"
+       , x = "Lineage"
+       , y = "DUET (PS)")
+
+
+#############
+#========================
+# Plot 3: DUET, lineage, or_mychisq
+# x = lineage y = DUET
+# col = Lineage
+# fill = country_code
+#========================
+
+### begin plot
+table(df$lineage)
+
+g = ggplot(df, aes(x = lineage
+                   , y = duet_scaled))
+g + geom_point(aes(col = lineage
+                   , size = or_mychisq)) +
+  theme(axis.text.x = element_text(size = 13
+                                   , angle = 90
+                                   , hjust = 1
+                                   , vjust = 0.4)
+        , axis.text.y = element_text(size = 15
+                                     , angle = 0
+                                     , hjust = 1
+                                     , vjust = 0)
+        , axis.title.x = element_text(size = 15)
+        , axis.title.y = element_text(size = 15) ) +
+  labs(title = "DUET, lineage, or_mychisq"
+       , x = "Lineage"
+       , y = "DUET (PS)")
+
+#========================
+# Plot 4-6: Distributions
+# ggrdiges
+#========================
+
+df$country_code_symbols = as.character(df$country_code)
+foo = df
+
+foo = foo%>%
+  add_count(country_code)
+
+n = which(colnames(foo) == "n")
+colnames(foo)[n] = "count_country"
+
+
+table(foo$count_country)
+
+
+check = as.data.frame(cbind(foo$country_code_symbols, foo$count_country))
+str(check)
+check$V2 = as.numeric(check$V2)
+min(check$V2); max(check$V2)
+table(check$V2)
+
+check2 = subset(check, check$V2>100)
+check2 = subset(check2, is.na(check2$V1))
+min(check2$V2); max(check2$V2)
+
+check3 = subset(check2, check2$V1 != "")
+table(check3$V1 != "")
+
+
+# subset df with country containing >100 samples
+# and no missing 
+
+#%%%%%%%%%%%%%%%%%%%%%%%%
+# REASSIGNMENT
+df2 = df
+#%%%%%%%%%%%%%%%%%%%%%%%%
+df2 = df2%>%
+  add_count(country_code)
+
+str(df2$country_code); str(df2$n)
+
+n = which(colnames(df2) == "n")
+colnames(df2)[n] = "count_country"
+
+table(df2$count_country>100 & df$country_code!= "")
+df3 = subset(df2, df2$count_country>100 & df2$country_code != "")
+
+
+#%%%%%%%%%%%%%%%%%%%%%%%%
+# REASSIGNMENT
+df = df3
+#%%%%%%%%%%%%%%%%%%%%%%%%
+
+#==================================================
+my_ats = 15 # axis text size
+my_als = 20 # axis label size
+
+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'
+                     )
+      
+
+#========================
+# Plot 4: Distribution
+# x = duet_scaled
+# y = country
+# fill = country_code
+# facet = lineage
+#========================
+# works neatly!
+
+p1 = ggplot(df, aes(x = duet_scaled
+                    , y = country_code))+
+  
+  #printFile=geom_density_ridges_gradient(
+  geom_density_ridges_gradient(aes(fill = country_code)
+                               , scale = 3
+                               , size = 0.3 ) +
+  facet_wrap( ~lineage
+              , scales = "free"
+              , switch = 'x'
+              , labeller = labeller(lineage = my_labels)
+              ) +
+  coord_cartesian( xlim = c(-1, 1)) +
+  #scale_fill_gradientn(colours = c("#f8766d", "white", "#00bfc4")
+  #                     , name = "DUET" ) + 
+  theme(axis.text.x = element_text(size = my_ats
+                                   , angle = 90
+                                   , hjust = 1
+                                   , vjust = 0.4)
+        
+        #, axis.text.y = element_blank()
+        , 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)
+  ) 
+
+p1
+
+
+#========================
+# Plot 5: Distribution
+# x = duet_scaled
+# y = country_code
+# fill = lineage
+# facet = NONE
+#========================
+# no facet wrap
+
+p2 = ggplot(df, aes(x = duet_scaled
+                    , y = country_code))+
+  
+  geom_density_ridges_gradient(aes(fill = factor(lineage))
+                               , scale = 3
+                               , size = 0.3 ) +
+  coord_cartesian( xlim = c(-1, 1)) +
+  #scale_fill_gradientn(colours = c("#f8766d", "white", "#00bfc4")
+  #                     , name = "DUET" ) + 
+  #scale_fill_continuous(colours = c("darkgreen", "pink", "orange", "brown")
+  #                     , name = "lineage" ) + 
+  theme(axis.text.x = element_text(size = my_ats
+                                   , angle = 90
+                                   , hjust = 1
+                                   , vjust = 0.4)
+        
+        #, axis.text.y = element_blank()
+        , 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)
+  ) 
+
+p2
+