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philippbayer/My_data.tsv

Last active January 2, 2019 10:14
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This is the data and the plot I used for my PAG poster on repeatmasking problems in R-gene prediction.
Raw
My_data.tsv
Class Repeatmasking Assembly Count
CNL before B. napus 23
CNL after B. napus 13
CNL before B. rapa 20
CNL after B. rapa 10
CN before B. napus 47
CN after B. napus 25
CN before B. rapa 16
CN after B. rapa 5
N before B. napus 92
N after B. napus 43
N before B. rapa 26
N after B. rapa 13
NL before B. napus 48
NL after B. napus 12
NL before B. rapa 12
NL after B. rapa 5
TN before B. napus 74
TN after B. napus 7
TN before B. rapa 27
TN after B. rapa 0
TNL before B. napus 125
TNL after B. napus 2
TNL before B. rapa 72
TNL after B. rapa 0
Raw
plot.R
repeats <- read.table('./My_data.tsv',head=T, sep='\t')
library(ggplot2)
ggplot(data=repeats,aes(x=Repeatmasking, y=Count, group=interaction(Class,Assembly), colour=Assembly, shape=Class))+
ylab("Predicted R-genes") +
xlab('Repeat-masking') +
geom_point(size=3)+
geom_line()+
scale_x_discrete(limits=c('before', 'after')) +
theme_light() + scale_color_brewer(palette='Set1')
# optionally, once can facet by assembly:
# + facet(~Assembly)
ggsave(filename = 'Repmasking_before_after.png', device = 'png', dpi = 300, units = 'cm', height=13,width=15)
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