plot_single_cell

Reliability status: deprecated ?

produces movies and structures from single cell PWD matrices

This scripts: - produces movies and trajectories from single cell PWD matrices. - calculates barcode detection efficiencies and number of barcodes per cell. - plots single cell matrices. - plots distance histograms and distributions of Rg.

usage: plot_single_cell [-h] [-F ROOTFOLDER] [-O OUTPUTFOLDER] [-P PARAMETERS]
                        [-A LABEL] [-W ACTION] [--fontsize FONTSIZE]
                        [--axisLabel] [--axisTicks] [--barcodes]
                        [--nRows NROWS] [--pixelSize PIXELSIZE]
                        [--maxDistance MAXDISTANCE]
                        [--plottingFileExtension PLOTTINGFILEEXTENSION]
                        [--shuffle SHUFFLE] [--ensembleMatrix]
                        [--plotHistogramMatrix] [--minNumberPWD MINNUMBERPWD]
                        [--threshold THRESHOLD]

Named Arguments

-F, --rootFolder

Folder with dataset

-O, --outputFolder

Folder for outputs

-P, --parameters

Provide name of parameter files. folders_to_load.json assumed as default

-A, --label

Add name of label (e.g. doc)

-W, --action

Select: [all], [labeled] or [unlabeled] cells plotted

--fontsize

Size of fonts to be used in matrix

--axisLabel

Use if you want a label in x and y

Default: False

--axisTicks

Use if you want axes ticks

Default: False

--barcodes

Use if you want barcode images to be displayed

Default: False

--nRows

The number of cells is set by nRows**2

--pixelSize

Pixel Size in um

--maxDistance

Maximum distance for histograms, in um

--plottingFileExtension

By default: svg. Other options: pdf, png

--shuffle

Provide shuffle vector: 0,1,2,3… of the same size or smaller than the original matrix. No spaces! comma-separated!

--ensembleMatrix

Use if you want ensembleMatrix to be plotted alongside sc matrices

Default: False

--plotHistogramMatrix

Use if you want to plot the PWD histograms for all bin combinations. This is slow!

Default: False

--minNumberPWD

Minimum number of PWD to calculate Rg

--threshold

Maximum accepted PWD to calculate Rg, in px