254 lines
7.3 KiB
R
254 lines
7.3 KiB
R
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#########################################################
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# 1: Installing and loading required packages
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#########################################################
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#source("../Header_TT.R")
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install.packages("qqman")
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library(qqman)
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source("combining_dfs_plotting.R")
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#mcsm_data: raw file, 225, 15
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#merged_df2 = 2201, 35
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#merged_df3 = 205, 35 ("Can't trust non-numerical params')
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#===============================================
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# PLOTS: DUET vs GWAS: non-numerical
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# lineage, country_code, etc
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# merged_df2: 1592, 35
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#===============================================
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#########################
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# Data for plot
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#########################
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df = merged_df2
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#df = merged_df2_comp
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#========================
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# Plot 1a: Lineage barplot
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# x = lineage y = No of samples
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# col = Lineage
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# fill = lineage
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#========================
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table(df$lineage)
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# subset only lineages1-4
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sel_lineages = c("lineage1"
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, "lineage2"
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, "lineage3"
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, "lineage4"
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#, "lineage5"
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#, "lineage6"
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#, "lineage7"
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)
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# uncomment as necessary
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df_lin = subset(df, subset = lineage %in% sel_lineages )
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table(df_lin$lineage)
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#%%%%%%%%%%%%%%%%%%%%%%%%%
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# REASSIGNMENT
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df <- df_lin
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#%%%%%%%%%%%%%%%%%%%%%%%%%
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#%%%%%%%%%%%%%%%%%%%%%%%%
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# REASSIGNMENT
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df2 = df
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#%%%%%%%%%%%%%%%%%%%%%%%%
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df2 = df2%>%
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add_count(country_code)
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str(df2$country_code); str(df2$n)
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n = which(colnames(df2) == "n")
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colnames(df2)[n] = "count_country"
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table(df2$count_country>100 & df$country_code!= "")
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df3 = subset(df2, df2$count_country>100 & df2$country_code != "")
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#%%%%%%%%%%%%%%%%%%%%%%%%
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# REASSIGNMENT
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df = df3
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#%%%%%%%%%%%%%%%%%%%%%%%%
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sample = sum(table(unique(df$id))); sample
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table(df$country_code)
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tab = sum(table(df$country_code)); tab
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View(table(df$country_code))
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View(t1)
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############## begin plot
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g = ggplot(df, aes(x = lineage))
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g + geom_bar(aes(fill = lineage)) +
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theme( axis.text.x = element_text(size = 13
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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 = 15
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, angle = 0
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, hjust = 1
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, vjust = 0)
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, axis.title.x = element_text(size = 15)
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, axis.title.y = element_text(size = 15) ) +
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labs(title = "Lineage"
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, x = "Lineage"
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, y = "No of samples")
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#========================
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# Plot 2: DUET, lineage, country_code and or_mychisq
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# x = lineage y = DUET
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# col = Lineage
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# fill = country_code
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#========================
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### begin plot
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g = ggplot(df, aes(x = country_code
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, y = duet_scaled))
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g + geom_point(aes(col = lineage
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, size = or_mychisq)) +
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theme(axis.text.x = element_text(size = 13
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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 = 15
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, angle = 0
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, hjust = 1
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, vjust = 0)
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, axis.title.x = element_text(size = 15)
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, axis.title.y = element_text(size = 15) ) +
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labs(title = "DUET, country_code, lineage, or_mychisq"
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, x = "Lineage"
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, y = "DUET (PS)")
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#############
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#========================
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# Plot 3: DUET, lineage, or_mychisq
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# x = lineage y = DUET
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# col = Lineage
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# fill = country_code
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#========================
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### begin plot
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table(df$lineage)
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g = ggplot(df_lin, aes(x = lineage
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, y = duet_scaled))
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g + geom_point(aes(col = lineage
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, size = or_mychisq)) +
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theme(axis.text.x = element_text(size = 13
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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 = 15
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, angle = 0
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, hjust = 1
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, vjust = 0)
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, axis.title.x = element_text(size = 15)
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, axis.title.y = element_text(size = 15) ) +
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labs(title = "DUET, lineage, or_mychisq"
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, x = "Lineage"
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, y = "DUET (PS)")
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#========================
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# Plot 4-5: Distributions
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# ggrdiges
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#========================
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#==================================================
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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_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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#========================
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# Plot 4: Distribution
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# x = duet_scaled
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# y = country
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# fill = country_code
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# facet = lineage
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#========================
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# works neatly!
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p1 = ggplot(df, aes(x = duet_scaled
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, y = country_code))+
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#printFile=geom_density_ridges_gradient(
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geom_density_ridges_gradient(aes(fill = country_code)
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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)
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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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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-5)
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, legend.title = element_text(size = my_als)
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)
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p1
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#========================
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# Plot 5: Distribution
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# x = duet_scaled
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# y = country_code
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# fill = lineage
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# facet = NONE
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#========================
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# no facet wrap
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p2 = ggplot(df, aes(x = duet_scaled
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, y = country_code))+
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geom_density_ridges_gradient(aes(fill = factor(lineage))
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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_gradientn(colours = c("#f8766d", "white", "#00bfc4")
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# , name = "DUET" ) +
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#scale_fill_continuous(colours = c("darkgreen", "pink", "orange", "brown")
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# , name = "lineage" ) +
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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-5)
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, legend.title = element_text(size = my_als)
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)
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p2
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