Update Tridimensional barplots in R/barplot_with_dots.R, Tridimensional...

Update Tridimensional barplots in R/barplot_with_dots.R, Tridimensional barplots in R/experimental_data.txt, Tridimensional barplots in R/initial.png, Tridimensional barplots in R/melted.png, Tridimensional barplots in R/plot_inR.png, Tridimensional barplots in R/savedplot.png, Tridimensional barplots in R/mybarplot.pdf files

Tridimensional barplots in R/barplot_with_dots.R

+mydata <- read.delim("experimental_data.txt", stringsAsFactors = F)
+#strain  vector  exp1  exp2  exp3
+# 1      wt vector1 0.981 1.011 1.008
+# 2      wt vector2 0.712 0.724 0.818
+# 3      wt vector3 0.135 0.426 0.402
+# 4      wt vector4 0.161 0.426 0.369
+# 5    mutA vector1 1.028 1.089 1.171
+# 6    mutA vector2 0.972 1.096 1.193
+# .....
+
+library(reshape2)
+# convert the table to a "longer" data format, but preserve
+# the dimensions that will be useful for plotting, here by index
+melted <- melt(mydata, id.vars=c(2,1))
+names(melted) <- c("vector", "strain", "experiment", "value")
+# vector strain experiment value
+# 1  vector1     wt       exp1 0.981
+# 2  vector2     wt       exp1 0.712
+# 3  vector3     wt       exp1 0.135
+# 4  vector4     wt       exp1 0.161
+# 5  vector1   mutA       exp1 1.028
+# 6  vector2   mutA       exp1 0.972
+# 7  vector3   mutA       exp1 0.141
+# 8  vector4   mutA       exp1 0.292
+# .....
+
+melted$strain <- factor(x=melted$strain, levels=c("wt", "mutA", "mutB"))
+# manually setting the "strain" as a factor with the levels in a given order
+# ensures that the plotting of thses categories will be done in this order
+
+library(dplyr)
+# compute mean and standard deviation of values, grouped by vector AND strain
+averages <- melted %>% group_by(vector, strain) %>% summarise(avg=mean(value))
+sds <- melted %>% group_by(vector, strain) %>% summarise(sd=sd(value))
+# create columns that will serve for the range of the error bars
+averages$ymin <- averages$avg-sds$sd
+averages$ymax <- averages$avg+sds$sd
+
+# changing the position of the bars in the barplot by the same amount
+# is crucial to align the dots, error bars and bars.
+# the following value is used three times in the plot, adjust to your liking
+dodge_value <- 0.8
+
+ggplot(data=averages, 
+       aes(x=vector, y=avg, color=strain, fill=strain))+
+  geom_col(width=0.7, position = position_dodge(dodge_value))+
+  scale_fill_manual(values = rep(c("gray30", "gray70", "white"), 4))+
+  # this needs to be adjusted and modified according to your needs
+  # for 4 vectors and 3 strains, three shades of gray can be enough
+  scale_color_manual(values = rep("black", 12))+
+  # this parameter ensures that error bars and bar outlines are all black
+  geom_point(data=melted, 
+             aes(x=vector, y=value, color=strain), 
+             shape=21, fill="white", 
+             position=position_jitterdodge(dodge.width=dodge_value, jitter.width = 0.3))+
+  # add the data points. Even if the color is black for all the points, that aesthetic
+  # parameter is required to tell ggplot2 that we want grouping by strain
+  geom_errorbar(data=averages, 
+                aes(ymin=ymin, ymax=ymax),
+                position = position_dodge(dodge_value),
+                width=0.2)+
+  # error bars, as SD
+  ylim(0, 1.4)+
+  # axis limits, to be adjusted to the range of the data, or remove to do it automatically
+  # the following parameters affect the plot and are especially useful for the pdf output
+  theme_classic(base_size=10)+
+  theme(text=element_text(size=6, family="ArialMT"), legend.key.size = unit(0.3, 'cm'))
+
+ggsave("mybarplot.pdf", width=8, height=5, units="cm")

Tridimensional barplots in R/experimental_data.txt

+strain	vector	exp1	exp2	exp3
+wt	vector1	0.981	1.011	1.008
+wt	vector2	0.712	0.724	0.818
+wt	vector3	0.135	0.426	0.402
+wt	vector4	0.161	0.426	0.369
+mutA	vector1	1.028	1.089	1.171
+mutA	vector2	0.972	1.096	1.193
+mutA	vector3	0.141	0.311	0.385
+mutA	vector4	0.292	0.349	0.331
+mutB	vector1	1.054	1.078	1.07
+mutB	vector2	0.573	0.834	0.683
+mutB	vector3	1.063	0.986	0.947
+mutB	vector4	0.679	0.804	0.616