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change prefix behaviour #9

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change prefix behaviour #9

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0e0c358
start debugging
sjanssen2 Aug 29, 2019
9c337b8
switch off visualizeFeature
sjanssen2 Aug 29, 2019
2ac4dc6
switch off all other file writes
sjanssen2 Aug 29, 2019
e90e4e4
print num features
sjanssen2 Aug 29, 2019
74fe355
limit to 3 features
sjanssen2 Aug 29, 2019
1d1f62c
remove double use of prefix
sjanssen2 Aug 29, 2019
beebdf3
remove double use of prefix
sjanssen2 Aug 29, 2019
45024c0
remove debug info and switch on feature file writes
sjanssen2 Aug 29, 2019
9dfd4cc
print name of program: back in
sjanssen2 Aug 29, 2019
63c0a81
nice
sjanssen2 Aug 29, 2019
4e57d89
whitespace
sjanssen2 Aug 29, 2019
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6 changes: 3 additions & 3 deletions R/Metalonda.R
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Original file line number Diff line number Diff line change
Expand Up @@ -46,7 +46,7 @@ metalonda = function(Count, Time, Group, ID, n.perm = 500, fit.method = "nbinomi
prefix = "Test")
{
cat("Start MetaLonDA \n")

if (!dir.exists(prefix)){
dir.create(file.path(prefix))
}
Expand Down Expand Up @@ -333,10 +333,10 @@ metalondaAll = function(Count, Time, Group, ID, n.perm = 500,
summary.tmp$dominant[which(summary.tmp$dominant == -1)] = gr.2

## Output table and figure that summarize the significant time intervals
write.csv(summary.tmp, file = sprintf("%s/%s_MetaLonDA_TimeIntervals.csv", prefix, prefix), row.names = FALSE)
write.csv(summary.tmp, file = sprintf("%s/MetaLonDA_TimeIntervals.csv", prefix), row.names = FALSE)
visualizeTimeIntervals(interval.details = summary.tmp, prefix, unit = time.unit, col = col)

aggregateData = list(output.detail = detailed, output.summary = summary.tmp, output.model = model)
save(aggregateData, file = sprintf("%s/%s_MetaLonDA.RData", prefix, prefix))
save(aggregateData, file = sprintf("%s/MetaLonDA.RData", prefix))
return(aggregateData)
}
2 changes: 1 addition & 1 deletion R/Visualization.R
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Expand Up @@ -214,7 +214,7 @@ visualizeTimeIntervals = function(interval.details, prefix = "Test", unit = "day
panel.grid.major.y = element_line(colour = "white", size = 6),
panel.grid.major.x = element_line(colour = "white",size = 0.75)) +
theme(legend.position="top", panel.border = element_rect(colour = "black", fill = NA, size = 2))
ggsave(filename = paste(prefix, "/", prefix, "_MetaLonDA_TimeIntervals.jpg", sep=""), dpi = 1200, height = 30, width = 20, units = 'cm')
ggsave(filename = paste(prefix, "/MetaLonDA_TimeIntervals.jpg", sep=""), dpi = 1200, height = 30, width = 20, units = 'cm')
}


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