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Advanced: Analysis Display Parameters
Robert F Cooper edited this page May 2, 2026
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Nearly all of the analyses performed by 𝑓(Cell) produce graphical plots or images of the results. In this section, we will go through the different outputs available in this version of 𝑓(Cell), as well as how to modify their appearance.
There are numerous possible outputs:
- A "population-based" summary of the iORGs, where all summaries are displayed overlapping on a single plot.
- A "population-based" summary of the iORGs, where all summaries are displayed according to their order of acquisition (so for 10 acquisitions in 3 trials, it would display 10 plots, with 3 summaries in each).
- "Individual-cell" summaries of the iORGs, where all acquisitions for each query location are combined, then displayed in aggregate (e.g. a histogram).
- "Individual-cell" summaries of the iORGs, where all acquisitions for each query location are combined, then displayed overlapping on a single plot.
| Key | Parent Key | Type | Options | Description |
|---|---|---|---|---|
"legend" |
"axes" |
boolean |
(**false**, true) |
Whether or not to display the plot's legend. |
"pop_summary_overlap" |
"display_params" |
JSON Object |
none |
A JSON object holding parameters for to the "population-based" summary of the iORGs. |
"pop_summary_seq" |
"display_params" |
JSON Object |
none |
A JSON object holding parameters for "population-based" summary of the iORGs, but plotted "end-to-end" |
"indiv_summary" |
"display_params" |
JSON Object |
none |
A JSON object holding parameters for individual-cell" summaries of the iORGs. |
"indiv_summary_overlap" |
"display_params" |
JSON Object |
none |
A JSON object holding parameters for individual-cell" summaries of the iORGs, plotted overlapping each other. |
Each of the above outputs can have its plot appearances extensively customized.
| Key | Parent Key | Type | Options | Description |
|---|---|---|---|---|
"xmin" |
"axes" |
float |
**null** |
The minimum X-axis value displayed on the plot/image. If null, then the X-axis minimum is determined according to the rules defined by Matplotlib. |
"xmax" |
"axes" |
float |
**null** |
The maximum X-axis value displayed on the plot/image. If null, then the X-axis maximum is determined according to the rules defined by Matplotlib. |
"ymin" |
"axes" |
float |
**null** |
The minimum Y-axis value displayed on the plot/image. If null, then the Y-axis minimum is determined according to the rules defined by Matplotlib. |
"ymax" |
"axes" |
float |
**null** |
The maximum Y-axis value displayed on the plot/image. If null, then the Y-axis maximum is determined according to the rules defined by Matplotlib. |
"cmap" |
"axes" |
"string" |
(**"plasma"**, any) |
Any colormap string (recognized by Matplotlib)[https://matplotlib.org/stable/gallery/color/named_colors.html]. |
"legend" |
"axes" |
boolean |
(**false**, true) |
Whether or not to display the plot's legend. |