tinyRNA provides an all-in-one solution for precision analysis of sRNA-seq data. At the core of tinyRNA is a highly flexible counting utility, tiny-count, that allows for hierarchical assignment of reads to features based on positional information, extent of feature overlap, 5’ nucleotide, length, and strandedness.
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tiny-plot: user-defined view limits for DGE scatter plots, and other consistency improvements #273
This PR adds options for user-specified min and/or max view limits for DGE scatter plots, which are specified as log2 count values and can be whole or fractional numbers. It also includes minor changes to output filenames from tiny-deseq and tiny-plot to be consistent with the "experimental condition vs. control condition" order used in DGE scatter plots. Plot titles and axis labels in bar plots have been updated to have sentence case, to be consistent with the scatter plots.
The following minor bugs have also been addressed:
A bug in lower view limit calculation that occurs when the feature with the lowest count also has a count of zero in another group/replicate (for DGE scatter plots and replicate scatter plots, respectively). Under certain conditions this could lead to the lowest count feature being clipped from the plot space. This is usually a non-issue due to the axes margins.
A divide by zero edge case for certain data limits while calculating major tick locations in scatter plots
The plot's true viewLimits are now used when placing major ticks (previously the data limit was used for the upper bound, but the view limit includes a margin if calculated automatically). This results in slightly more liberal placement of upper tick marks
The Run Config template in the testdata folder had not included the recently-added DGE class filtering options
This PR adds options for user-specified min and/or max view limits for DGE scatter plots, which are specified as log2 count values and can be whole or fractional numbers. It also includes minor changes to output filenames from tiny-deseq and tiny-plot to be consistent with the "experimental condition vs. control condition" order used in DGE scatter plots. Plot titles and axis labels in bar plots have been updated to have sentence case, to be consistent with the scatter plots.
The following minor bugs have also been addressed:
Closes #271