Skip to content

Visualization

The Visualization tab generates summary plots from quantification exports.

Interface overview

Input section

Controls:

  • Input folder (browse field): Folder containing quantification tables (.csv, .xlsx, .xls).
  • Extensions (text field): File extensions to search for in the input folder.

Behavior notes:

  • SenoQuant reads the first matching table to discover marker columns.
  • Marker columns are detected from headers ending with _mean_intensity.
  • If a JSON file is present, threshold values are auto-loaded when possible.

Marker selection and thresholding section

Controls:

  • Select all / Deselect all (buttons): Toggle all marker include checkboxes.
  • Include (checkbox per row): Include marker in downstream plotting.
  • Marker (read-only): Marker name parsed from quantification columns.
  • Threshold (text field per row): Numeric threshold value for each selected marker.

Behavior notes:

  • Thresholds are applied per marker before plotting.
  • If a thresholds JSON is found in the input folder, SenoQuant auto-fills matching marker thresholds.

Plots section

Controls:

  • Plot type (dropdown): Select the visualization type.

Available plot types:

  • Spatial Plot
  • UMAP
  • Double Expression
  • Neighborhood Enrichment

Plot preview section

Controls:

  • Process (button): Generate preview outputs using current settings.

Behavior notes:

  • PNG plots are shown directly in the preview pane.
  • SVG and PDF plots are shown as clickable links.
  • Running Process again clears previous previews.

Output section

Controls:

  • Output path (browse field): Destination folder for saved plots.
  • Plot name (text field): Base name for saved files.
  • Format (dropdown): png, svg, or pdf.
  • Save plot (button): Copy the latest processed plots to the output folder.

Plot behavior details

Spatial Plot

  • Uses detected X/Y coordinate columns for point positions.
  • With selected markers, assigns each cell to the first marker (in marker list order) whose intensity is above threshold.
  • Cells that do not pass any selected marker threshold are labeled as Other.
  • Uses categorical colors (legend per assigned marker + Other).

UMAP

  • Uses selected marker intensity columns as UMAP input features.
  • Requires at least two numeric input columns.
  • Applies thresholds by clipping values below threshold to 0 before embedding.
  • Generates a 2D embedding scatter plot.

Double Expression

  • Requires exactly two selected markers.
  • Uses thresholds for each selected marker.
  • Draws:
  • Negative cells (background, light gray).
  • Marker 1 positive only (red).
  • Marker 2 positive only (blue).
  • Double positive (green).

Neighborhood Enrichment

  • Requires at least two selected markers with resolvable columns.
  • Builds a k-nearest-neighbor graph from X/Y coordinates and computes class-by-class enrichment z-scores.
  • Class assignment uses first-match marker precedence; unassigned cells are grouped as Negative.
  • Outputs a heatmap matrix with z-score annotations.

Output naming

  • If Plot name is set and a single output is produced, filename is <plot_name>.<ext>.
  • If multiple outputs are produced, filenames are <plot_name>_1.<ext>, <plot_name>_2.<ext>, etc.
  • If Plot name is blank, SenoQuant prefixes filenames with the plot type.

Tips

  • Use quantification outputs from the same image cohort for consistent marker columns.
  • Check X/Y coordinate column names in your exported tables if spatial plots return no output.
  • Keep marker thresholds available in a JSON file when possible to avoid manual entry on each run.
  • For Double Expression, make sure both selected markers exist as <marker>_mean_intensity.