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HRGV / phyloFlash

phyloFlash - A pipeline to rapidly reconstruct the SSU rRNAs and explore phylogenetic composition of an illumina (meta)genomic dataset.
GNU General Public License v3.0
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phyloFlash_compare.pl --barplot_scaleplotwidth not scaling #138

Closed ghost closed 2 years ago

ghost commented 3 years ago

I've run phyloflash on a number of samples and am trying to generate a barplot comparison. phyloFlash_compare.pl runs without errors/warnings, but the --barplot_scaleplotwidth is not adjusting the width of the graph, nothing is changing with it at values 4,6 vs without it at all.

is there a way to have more control over the dimensions of the plot created?

kbseah commented 3 years ago

hello @catarinaloureiro , phyloFlash_compare.pl --task barplot is a wrapper for phyloFlash_barplot.R. the scale plot width option is a bit of a hack. The actual width is a constant plus the number of bars times the scaling factor (see lines 191-192) of the R script. It's ultimately calling ggplot, so for finer control you could modify the R script or import the ....NTUabundance.csv files containing the abundance data to R or your preferred platform for your own plots or data exploration.