The results model¶
Both explorers present their results as a live table. This page explains what a row means and how the numbers and colours in the cells are produced. The tutorials Reading the results and Reading the coverage browser show the same ideas in the interface.
Rows are cell groups¶
A row is not a single sample. Each row is a cell group: the cells of one cell type within one combination of the active metadata columns, such as organ, disease, and study. Malva aggregates the matching samples into one row so that you can compare groups instead of thousands of individual samples.
The row label shows the cell type, and the metadata columns show the values that define the group. The Cells column counts the cells in the group.
Expression columns¶
Each search in your job adds one expression column. The cell of that column is a small plot that summarises the group for that search:
- A thin line spans the minimum to maximum expression value.
- A thicker bar spans the first to third quartile (the interquartile range, Q25 to Q75).
- A circle marks the median, and the circle's size encodes the fraction of cells in the group that express the sequence. A larger circle means a larger fraction.
Hovering over the cell shows the exact values: mean, median, quartiles, fraction, and the number of cells and samples.
Display modes¶
You can change what the expression columns show. The display mode applies to the whole table.
| Mode | Label | Meaning |
|---|---|---|
| Relative expression | Relative expression | ln(1 + 10E), where E is the group's mean expression with zeros included, divided by the per-sample median. The value ranges from 0 to 7. This is the default. |
| Fraction | Fraction expressing | The proportion of cells with detected expression, from 0 to 1. This measures breadth, not strength. |
| Raw counts | Raw kmer hits | The mean raw k-mer hit count per expressing cell, without normalisation. This reflects sequencing depth. |
| Cells | Cell count | The number of cells in the group. |
Colours¶
The background intensity of an expression cell encodes its value relative to the rest of the table. Colours always adapt to the current theme (light or dark), and you can choose a colour scale: blue, divergent, or viridis. The choice is a matter of taste; it never changes the underlying values.
Metadata columns and enrichment¶
The metadata columns of a row can be highlighted relative to the rest of the
visible rows. Malva marks values that appear more often (enriched) or less
often (depleted) than expected among the top-covered rows. A small label shows
the fold change and a q-value, for example 2.5x enriched (q = 0.01).
See What does the enrichment highlight mean? in the results tutorial for the exact thresholds.
The detail panel¶
Expanding a row opens a detail panel with the samples behind the group. It shows the number of cells and samples, offers Copy IDs, CSV, DOIs, and SRA buttons, and groups the samples by study. Clicking a sample opens its full metadata with links to external resources such as GEO and PubMed.
Coverage results¶
The Coverage Explorer uses the same row model, with one difference: the first column is a track that draws the coverage across the queried positions for that group, instead of a per-search expression plot. The Cells column and the metadata columns work exactly as above.
Filtering¶
You refine the table with metadata filters, numeric ranges, ontology filters, and free text. Filters do not consume quota, and you can save any combination of them as a group. See Filtering samples and Ontologies.