figure1 code

01_ploidy_spore_viability_aneuploidies/README

@@ -1,48 +1,36 @@
 Code and input files for plotting Figure 1: results of ploidy estimation, spore viability, large copy number variants and aneuploidies
 
 
-### Ploidy estimation measured with DNA staining & fluorescence
+plotFigure1.R
 
-plotPloidy.R
 
-requirements:
-./input_files/Ploidy_JT_tot.txt
+### Ploidy estimation measured with DNA staining & fluorescence
 
-output:
-plotPloidy.pdf
+./input_files/Ploidy_JT_tot.txt.gz
 
+./output/plotPloidy.pdf
 
 
-### Distribution of allele frequencies of single nucleotide variants in Jean-Talon
 
-plotFreq.R
+### Distribution of allele frequencies of single nucleotide variants in Jean-Talon
 
-requirements:
-./input_files/SNP_frequencies.tab
+./input_files/SNP_frequencies.tab.gz
 
-output:
-plotFreq.pdf
+./output/plotFreq.pdf
 
 
 
 ### Viable spores per tetrad
 
-plotDotplot.R
-
-requirements:
 ./input_files/sporulation_data.tab
 
-output:
-plotDotplot.pdf
+./output/plotDotplot.pdf
 
 
 
 ### Copy number in 250 bp windows across the Jean-Talon genome
 
-plotCNVsInGenome.R
 
-requirements:
-./input_files/formatInput_Jean-Talon.tab
+./input_files/formatInput_Jean-Talon.tab.gz
 
-output:
-plotCNVsInGenome.pdf
+./output/plotCNVsInGenome.pdf

01_ploidy_spore_viability_aneuploidies/plotFigure1.R

@@ -0,0 +1,139 @@
+
+### Plotting ploidy from DNA staining of the Jean-Talon colonies
+
+# author:Souhir Marsit
+library(ggplot2)
+library(dplyr)
+
+
+tab_total = read.table(gzfile('./input_files/Ploidy_JT_tot.txt.gz'), header = T, sep = '\t')
+tab_total= filter (tab_total, GRN.B.HLog> 2000)
+tab_ech= filter (tab_total, ech != 90)
+tab_ech= filter (tab_ech, ech != 93)
+tab_ech= filter (tab_ech, ech !=91)
+tab_ech= filter (tab_ech, ech != 92)
+tab_ech= filter (tab_ech, ech != 89)
+tab_ech= filter (tab_ech, ech != 96)
+tab_ech= filter (tab_ech, ech != 95)
+tab_ech= filter (tab_ech, ech != 94)
+tab_ech= filter (tab_ech, GRN.B.HLog> 5000)
+tab_ech= filter (tab_ech, ech != "ech")
+tab_ech = mutate (tab_ech, "rep"= "sampl")
+tab_ctl1= filter(tab_total, ech==90 )
+tab_ctl2= filter(tab_total, ech==93 )
+tab_ctl1 = mutate (tab_ctl1, "rep"= "ctl1")
+tab_ctl2 = mutate (tab_ctl2, "rep"= "ctl2")
+tab_tot = rbind (tab_ctl1, tab_ctl2, tab_ech)
+
+
+p <- ggplot(tab_tot, aes(x = GRN.B.HLog, colour = rep, group = ech, linetype = rep)) +
+  geom_density() + 
+  scale_colour_manual(values = c(ctl1 = "black", ctl2 = "black", sampl= "black", name="")) + 
+  scale_linetype_manual(values = c(ctl1 = "dotted", ctl2 = "longdash", sampl = "solid", name="")) +
+  xlim(0, 35000) +
+  labs(x = "Fluorescence (a.u.)", y = "Density") +
+  theme(panel.background = element_blank(),
+        panel.grid = element_blank(),
+        legend.position = "None",
+        legend.title = element_blank(),
+        axis.title = element_text(size = 20),
+        axis.text = element_text(size = 16))
+p
+
+
+pdf("./output/plotPloidy.pdf", onefile = T, width = 7, height = 7)
+p
+dev.off()
+
+
+
+### Plotting spore viability
+
+# author:aniafijarczyk
+library(ggplot2)
+library(dplyr)
+library(tidyr)
+
+#df <- read.table("./input_files/sporulation_data.tab", sep = "\t", header = TRUE)
+
+df <- data.frame("JT1" = c(1,2,0,2,0,2,1,2,1,2,0,1,3,1,2,1,3,0,0,2,1,2,1,0),
+                 "JT2" = c(2,3,1,1,2,2,1,2,2,0,1,1,2,2,1,1,0,1,2,1,0,2,1,0),
+                 "JT3" = c(2,1,0,2,1,4,1,2,2,2,0,0,0,2,2,1,2,1,1,2,0,2,1,1))
+dd <- df %>% gather(key = "Replicate", value = "Spores", JT1:JT3)
+
+
+p <-ggplot(dd) + aes(x = Replicate, y = Spores) +
+  geom_boxplot(fill = "grey80") +
+  geom_dotplot(binaxis='y', stackdir='center',dotsize=1.2, stackratio = 1) +
+  labs(x = "Replicates", y = "No. viable spores per tetrad") +
+  theme(panel.background = element_blank(),
+        panel.grid = element_blank(),
+        axis.title = element_text(size = 18),
+        axis.text.x = element_blank(),
+        axis.ticks.x = element_blank(),
+        axis.text.y = element_text(size = 18))
+p
+
+pdf("./output/plotDotplot.pdf",w=7,h=4)
+p
+dev.off()
+
+
+
+### Plotting frequencies of the Jean-Talon variants
+
+
+df <- read.table(gzfile("./input_files/SNP_frequencies.tab.gz"), sep = "\t", header=TRUE)
+
+p <- ggplot(df) + aes(x = FreqAlt) +
+  geom_histogram(colour = "white", fill = "black") +
+  labs(x = "Variant frequency", y = "No. variants") +
+  #ggtitle(label = " Frequency of mapped variants") +
+  theme(panel.background = element_blank(),
+        panel.grid = element_blank(),
+        plot.title = element_text(hjust = 0.5, size = 18),
+        axis.text = element_text(size = 16),
+        axis.title = element_text(size = 20))
+p
+
+pdf("./output/plotFreq.pdf",w=7,h=7)
+p
+dev.off()
+
+
+
+### Plotting coverage profile across Jean-Talon genome
+
+
+# Reading & filtering input
+
+df <- read.table(gzfile("./input_files/formatInput_Jean-Talon.tab.gz"), sep = "\t", header = TRUE)
+dff <- df %>% dplyr::filter(row_number() %% 3 != 1) ## Delete every 3rd row starting from 1
+
+
+# Plotting coverage
+p <- ggplot(dff)  +
+  geom_rect(data=df,aes(xmin = win_stop-250, xmax = win_stop, ymin = -Inf, ymax = Inf, fill = chrom)) +
+  scale_fill_manual(values = rep(c("white","grey80"),8)) +
+  geom_point(aes(x = win_stop-125, y = cn, colour = type), size = 0.1) +
+  scale_colour_manual(values = c("#D55E00", "#0072B2","grey20")) +
+  #facet_wrap(~chrom, ncol = 4) +
+  scale_x_continuous(expand = c(0, 0), breaks = c(115132.5,637066.5,1202495,2127210,3182043,3606023,4286949.5,5114076,5615542,6208748.5,6915625.5,7788439.5,8789909.5,9644448.5,10582321.5,11602066.5),
+                     labels = c("I","II","III","IV","V","VI","VII","VIII","IX","X","XI","XII","XIII","XIV","XV","XVI")) +
+  scale_y_continuous(limits = c(0,8)) +
+  #geom_text(data = dtext, aes(x = pos.x, y = pos.y, label = label)) +
+  labs(x = "Chromosomes", y = "Norm. copy number") +
+  theme(panel.background = element_blank(),
+        panel.grid = element_blank(),
+        legend.position = "none",
+        axis.text = element_text(size = 12),
+        axis.title = element_text(size = 14),
+        axis.ticks.x = element_blank())
+p
+
+
+# Saving plot
+pdf("./output/plotCNVsInGenome.pdf",w=12,h=3)
+p
+dev.off()
+