Version 0.2.7

Analysis addin:

• The Count Within worksheet includes summary counts across all tissue
  categories when multiple categories are reported.
• Fix chart report to run when "Total Cells" is the only phenotype
  defined (#32).
• Fix chart report to handle "All Cells" correctly.
• Fix H-Score report to always include every combination of
  Slide ID (or Sample Name) and Tissue Category.
• When computing mean expression for All tissue categories,
  don't propagate NA. The All numbers reflect the valid tissue categories.
• Fix to work with latest dplyr.

Spatial map viewer addin:

• Don't require Slide ID in the source cell data file.

Version 0.2.6

Analysis addin:

• Don't require tissue segmentation in the inForm project (#4).
• Add the ability to compute H-Score for individual phenotypes (#30).
  When selected, additional H-Score worksheets and charts will be created in the
  output reports.
• When "Use regular expressions" is checked, the regular expression will
  match anywhere in the Slide ID, not just the prefix.
• Fill in missing tissue categories so all slides have all categories
  reported (#1).
• Report missing / invalid values consistently as #N/A, never as #NUM.

Merge addin:

• Fix a problem that caused data corruption when cell seg data is
  formatted with comma as decimal separator (#31).

Misc:

• Use the RStudio folder chooser when available, rather than the Windows
  native chooser. The RStudio chooser is nicer and gives access to
  network drives (#29).

Version 0.2.5

Analysis addin:

• Reverse the y-axis of heatmaps so that the identity runs
  from the top left to bottom right.

Spatial map viewer improvements:

• Add "touching cells" visualization and related data.
• When saving plots, the viewer optionally saves the associated data (#22).
• Spatial map viewer works correctly with inForm data containing
  field coordinates (vs slide coordinates) (#16).

Consolidate and summarize addin:

• Add a Slide ID column with value "None" if none is present.

Component levels report:

• Optionally export data from pairs plots as TSV files.

Misc:

• Now requires tidyr >= 1.0.0.

Version 0.2.4

Spatial map viewer improvements:

• Dramatic improvement in time to render the charts, especially with 2x2 fields.

Analysis addin:

• Save nearest neighbor and count within detail as tab-separated text files
  instead of CSV files. This allows the detail files to be used as input
  to a second run of the analysis addin.
• Improved heatmaps in Charts output:
  • Maximum of eight heatmaps per page
  • Split the facet titles so the full Slide or Annotation ID is visible
• Better nearest_neighbor_summary
  • Avoid warnings from min and max and return NA for all values
    when there are no examples of a phenotype (#20).

Unmixing quality report:

• Tables show components as ordered in the data, not in alphabetical order.
• Pixel intensity chart uses actual pixel intensity as labels on the x-axis,
  rather than log10 values.

Component levels report:

• Charts use actual pixel intensity as labels on the x-axis,
  rather than log10 values.

Version 0.2.3

Spatial map viewer improvements:

• Calculates nearest neighbors on the fly
• Works with data from Consolidated_data.txt (doesn't need nearest_neighbors.csv)
• Supports multiple positivity and expressions in phenotype selectors!

Component levels report:

• Allow the user to enter the quantile(s) to display on the histograms.
  If two or more quantiles are entered, include a signal-to-noise table
  in the report, showing the ratio of the highest quantile to the lowest.

Bug fixes:

• Fixed a problem that caused the analysis addin to incorrectly report
  zero cells in a phenotype (#15).

Version 0.2.2

Spatial map viewer addin:

• New addin provides a field-based viewer of nearest neighbor relationships.
  See the Visualizing spatial relationships tutorial for details.

Analysis addin:

• Phenotype definitions may include valid expressions such as ~`Membrane PDL1 (Opal 520) Mean`>5.

Bug fixes:

• Fix error during calculation of N/A and Total cell in cell seg summary report

Version 0.2.0

Analysis addin:

• Add support for aggregation by a selectable column (#3). This allows
  reporting by Sample Name or Annotation ID as well as by Slide ID.
• Detailed output of nearest neighbors includes the Cell IDs of
  nearest neighbors as provided by phenoptr::find_nearest_neighbors.
• Recognize and correctly read inForm data
  which uses comma as the decimal separator.
  (Requires phenoptr >= 0.1.6.9000; related to akoyabio/phenoptr#8).
• More robust find_common_prefix function works with empty and
  numeric Slide IDs.

Bug fixes:

• Fix the way the analysis addin handles special characters in Slide ID (#9).
• Fix file chooser to work on RStudio Server.

Version 0.1.7

Analysis addin

• Optionally save nearest-neighbor and count-within details for each cell.
• Reverse the fill scale of the nearest neighbor heatmaps so red represents
  closer cells.
• Write session info to session_info.txt in the output directory.

Unmixing quality report

• Add "Guidance" section.

Component levels report

• Show a single quantile (99.9 percentile) in the signal histograms.
• Omit Autofluorescence from the pairs plots.
• Use a common scale on the individual plots within each pairs plot to
  avoid exaggerating small signals.
• Add "Guidance" section.
• Remove "Signal to noise" section.

Merge addin

• More forgiving handling of duplicated records.
  It now ignores the duplicates with a warning.
• Less noisy console output.

General

• Reports save temporary files in a subdirectory of the output directory (#5)
• File and directory choosers are cross-platform (#8)

Version 0.1.6

New features:

• Analysis app optionally creates tabular summaries and heatmap visualizations
  of nearest neighbor distance and count within radius for all phenotype pairs.
• Component levels report includes pair plots of component vs component
  for each source image.

Bug fixes:

• Component levels report
  • Write CSV files to the export directory, not its parent.
  • Fix height of "Pixel intensity by component" charts.
• Consolidate merged files
  • Fix to recognize "Annotation ID" as the field name.
• Analyze consolidated data
  • Update for dplyr 0.8 to fix #N/A values in Total lines of
    Cell Counts, Cell Percents and Cell Density sheets
• Clean up chart output
  • "All" tissue category is last in charts which have it, same as "Total".
  • Fix "Cell Count" axis label
  • Fix legend in H-Score chart - "name repair" in readxl version 1.2.0
    created unexpected column names which were shown in the legend.

Version 0.1.5

New features:

• The "Merge cell seg files" addin now supports searching sub-directories
  for target files.
• The "Consolidate and summarize" addin remembers the last directory
  for subsequent selections.
• More informative error message if consolidation fails due to mis-matched
  data files.

Bug fix:

• compute_density works with "square microns" spelled as inForm does.