tiny-plot: user-defined view limits for DGE scatter plots, and other consistency improvements#273
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taimontgomery merged 8 commits intomasterfrom Jan 13, 2023
Merged
tiny-plot: user-defined view limits for DGE scatter plots, and other consistency improvements#273taimontgomery merged 8 commits intomasterfrom
taimontgomery merged 8 commits intomasterfrom
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… are free to specify either or both values. Values are expected to match what the user sees on the labeled plot axes, i.e. the log2 normalized value rather than the raw count value. This commit also addresses a bug in the lower limit calculation that occurs when the feature with the lowest count also has a count of zero in another sample/group (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. get_scatter_view_lims() will report a warning if the values for axes.xmargin and axes.ymargin differ. The larger of the two values will be chosen if this happens.
… in filenames for tiny-deseq's DGE tables, and in tiny-plot's DGE scatter plots
… also includes a version bump since this PR represents the first functional change to tinyRNA since the v1.2.1 release
…slightly more liberal upper tick placement
…e plugin for PyCharm so that it doesn't crash when using conda-provided R on macOS
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Tested custom plot limits successfully with Lib303 dataset. File names and plot labels are correct. |
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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