Customize a Chart
Every chart in a figure panel is built for publication, not just for a quick look. The chart editor gives you the legend, the axes, the marks, the statistics, and the type sizes, so the chart that lands in your manuscript is the one you meant to draw.
Opening the Editor
Click Edit on any chart panel in a figure. The sidebar is a series of steps, and which ones you get depends on the chart:
- Choose data connects a project table or takes rows you type in
- Chart type picks the plot and the columns that feed it
- Axes & Labels covers titles, axis labels, scale, range, and ticks
- Clustering, on heatmaps only
- Comparisons, where error bars and significance tests apply
- Appearance holds everything visual
Changes preview live. There's no save button, and the back arrow at the top of the sidebar leaves the panel with what you set.
Tip: There are around sixty controls in here, so use the search box above the steps. Type "gridlines" or "error" and it lists the matches grouped by step, jumps you to the one you pick, and opens the group it lives in. It also tells you when a control exists but doesn't apply to your chart type, and why.
Controls that can't affect your chart aren't shown. A heatmap has no y-axis scale to set, so the field isn't there rather than sitting inert.
A plot drawn live from flow data is different: instead of these steps it offers the panel text plus a Plot section with the plot's own controls, scales and gate outlines included, described in Figures.
Chart Types
Twelve types: Bar, Grouped, Proportion, Box Plot, Histogram, Scatter, Violin, Dot Plot, Line, Heatmap, Paired, and Waterfall.
Charts are created in three places, with different powers. The Chart drawer in Data Tables and the results view of an image analysis both give you a quick preview with four controls, meant for looking rather than publishing. The figure editor, this page, is the only place appearance is edited. Charts produced by a flow or image analysis arrive with their own look already set, so their editor offers labels and layout but not the palette, since changing it would break the analysis's own color scheme.
Place and Size the Legend
The Legend group in Appearance controls where the key sits and how big it is.
- Position puts the legend on the top, bottom, left, or right of the plot, or hides it
- Alignment slides it along that side. A top or bottom legend aligns left, center, or right. A side legend aligns top, middle, or bottom. A bottom legend set to Left hugs the lower-left corner, which is the convention many journals ask for.
- Size sets its font size. Leave it blank for automatic sizing, which scales the legend with the panel.
Legend size is measured against the chart's own canvas rather than your screen, so a size you pick in the editor holds up in the exported figure and in a small multi-panel grid.
Tune the Axes
The Axes & Labels step carries:
- Chart title, which falls back to the panel letter if you leave it blank, and Panel subtitle beneath it
- Axis labels for each axis
- Y-axis scale and X-axis scale, switching between Linear and Log₁₀
- Y-axis range and X-axis range, with an explicit minimum and maximum so several panels can share one scale. Blank means automatic.
- Y-axis ticks and X-axis ticks, which take an approximate count and a format: automatic, a fixed number of decimals, or scientific notation
- X-axis labels, which keeps category names horizontal, angles them at 45°, stands them vertically, or wraps them onto several lines. They're never truncated.
- Show gridlines, in the same scale and range group. Turn it off for the clean, gridless look most journals prefer.
Panel annotation is here too: a block of free text placed along an edge of the panel, for the line every figure needs. Mean ± SEM on one line and Two-tailed Welch's t-test on the next is exactly what it's for.
Style the Marks
The Series group in Appearance changes with the chart type.
For line charts, set the line width, and a line style per series next to that series' color swatch, so solid, dashed, and dotted tell your series apart in grayscale print. Markers can be added to each point or left off.
For scatter, dot plots, and line charts, pick the marker shape and size.
For bar charts, Bar fill switches between a subtle gradient and a flat publication-style fill, and Show values on bars prints each bar's number above it. On a heatmap the same control reads Show values in cells.
Show Individual Data Points
A bar shows a mean, and two very different datasets can produce the same bar. Reviewers increasingly want the underlying measurements visible.
Turn on Show individual points and every bar, box, and violin gets its raw values scattered over it as small jittered dots, sized by their own control. The dots sit above the mark but below the error bars and any significance brackets.
When your table has a group column, each bar is the mean of the rows in that group and the dots are exactly those rows. With one value per category you get one dot per bar, which reads as a sanity check rather than a distribution.
The toggle is disabled on a chart with no raw values behind it, which happens with pre-summarized analysis results. The note says what to do: re-save the chart from its data.
Error Bars and Significance
The Comparisons step appears on chart types that can carry it.
Error Bars offers standard deviation, standard error, or a 95% confidence interval.
Statistical Test picks the test: Welch's t-test, Mann-Whitney U, a paired t-test, or Wilcoxon signed-rank. With three or more series you also get ANOVA with post-hoc t-tests, Kruskal-Wallis with post-hoc Mann-Whitney, and two-way ANOVA where the data supports it.
Multiple Comparison Correction appears once there's more than one comparison, offering Bonferroni, Holm, or Benjamini-Hochberg FDR. Reach for it: running six pairwise tests and reporting raw p-values is the most common statistical error in a figure.
P-value brackets then draws the comparisons you build, pair by pair, above the marks.
Heatmap Clustering
Heatmaps get their own step. Cluster rows and Cluster columns reorder the matrix so similar profiles sit together, and turning either on reveals two more choices: Linkage (average, which is UPGMA, complete, or single) and Distance (Euclidean or correlation).
Correlation distance is usually what you want when the shape of a profile matters more than its magnitude, such as expression across conditions.
Set Type Sizes
Font sizes live in two places. Title & subtitle size is in the Axes & Labels step, next to the text it applies to. Axis label size and tick label size are in the Text group at the bottom of Appearance.
Sizes are in the chart's own units, so they stay proportional when the figure exports at higher resolution or when a panel shrinks inside a dense grid.
Colors
The Colors group sets the palette for the whole chart: Classic, Colorblind Safe, Nature, Grayscale, or Vivid, with a swatch per series you can override. A single-series bar chart colors its bars by category instead, so the palette is actually visible.
Heatmaps get a Color Scale choice instead: Sequential for values running low to high in one direction, or Diverging for values centered on zero that go both ways.
Tip: Colorblind Safe isn't a compromise. It reads correctly for the roughly one reader in twelve who needs it, and it survives being printed in greyscale, which the default palette doesn't.