NEWS

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geyser 1.5.1

Document pandoc dependency. Increment version to match (?) bioconductor.

geyser 1.3.7

Fixed bug in x and y axis labeling (they were swapped)

geyser 1.3.6

Add in checkbox controls in the config options.

Add some text to the readme explaining what fields are available to auto configure within the SummarizedExperiment object

geyser 1.3.5

• Add check.names = FALSE to all data.frame() calls to better handle special characters.
• The heatmap view defaults to mean grouping by the user selected metadata values
• Fix bug in group filtering logic

geyser 1.3.4

• New config capability to pre-select plotting options (e.g. genes, assay slot, sample groupings). Can also output a configuration file based on the current customization.

• Plotting options can also be loaded in via the via metadata(rse)$geyser_config as a list

• Heatmap can now optionally flip axes and can collapse individual samples to the group level

geyser 1.3.3

• Geyser looks for information in the $metadata slot to print on the loading screen.
• Faceting adds in user-selected rowData info (instead of being hardcoded to rowname).
• Fixed bug in point labels where it was not adjusting to the y-axis jitter.

geyser 1.3.1

Geyser now has the ability to load an SCE from an .rds file (when called with geyser(), no arguments). Geyser now has color palettes (pals and ggplot2), custom plot height, optional points plotting, metadata-group based filtering, and optional point text labeling. Point spread logic was changed from geom_beeswarm to geom_quasirandom as I found the former had some odd behavior with point spread in larger sample datasets. Geyser now has a persistent file loader.

geyser 1.3.0

BioConductor release

geyser 0.99.8

Add BiocStyles to import (failed on "nebbiolo1" automated build testing)

geyser 0.99.7

• User can now select features (rows) from the rowData slot. Previously was only using the row.names of the SummarizedExperiment object

geyser 0.99.6

• Make some internal column names more unique, change license to CC0

geyser 0.99.5

• factor order respected in heatmap also (previously was just the dot plot)

geyser 0.99.4

• xlab text matches slot selected
• factor order respected for (SINGLE) sample grouping in plot
• optional color for a single column

geyser 0.99.3

• updated bslib requirement to >= 0.6.0
• replaced a "=" with "->"
• fixed empty comma error in the Shiny UI
• tweak wording and plot size in the plotting view

geyser 0.99.2

• addressing https://github.com/Bioconductor/Contributions/issues/3107 - Thanks
• replaced T/F with TRUE/FALSE
• fixed bug in vignette example (removed unnecessary SummarizedExperiment call) - Thanks @federicomarini
• added inst/extdata/make_tiny_rse.R which reproduces the tiny_rse example data
• changed vignette style to BiocStyle::html_document
• updated DESCRIPTION with urls
• reduce full import of outside packages
• Expanded unit testing suite for the box plot and heatmap generating functions
• lightly refactored the internal .exp_plot and .hm_plot functions to stop weird errors with testthat unit testing

geyser 0.99.1

• fixed bug in vignette yaml

geyser 0.99.0

• submitted to Bioconductor

geyser 0.30.0

• Added a NEWS.md file to track changes to the package.
• Restructure ui.R/server.R to put the code directly into geyser::geyser.R to better match bioconductor style
• Better error handling for low value rows
• Removed one "in app" guide as the info is in the vignette