plot_bootstrapping

Reliability status: development

Perform bootstrapping analysis on PWD distance matrices.

INPUTS: - PWD single cell maps in npy - uniquebarcode list

usage: plot_bootstrapping [-h] [-T INPUT] [-U UNIQUEBARCODES]
                          [-O OUTPUTFOLDER] [--fontsize FONTSIZE]
                          [--axisLabel] [--cMin CMIN] [--cMax CMAX]
                          [--cMin_std CMIN_STD] [--cMax_std CMAX_STD]
                          [--plottingFileExtension PLOTTINGFILEEXTENSION]
                          [--shuffle SHUFFLE] [--cmap CMAP]
                          [--cmap_std CMAP_STD] [--N_bootstrap N_BOOTSTRAP]

Named Arguments

-T, --input

Filename of single-cell PWD matrices in Numpy

-U, --uniqueBarcodes

csv file with list of unique barcodes

-O, --outputFolder

Folder for outputs

--fontsize

Size of fonts to be used in matrix

--axisLabel

Use if you want a label in x and y

Default: False

--cMin

Colormap min scale. Default: 0

--cMax

Colormap max scale. Default: automatic

--cMin_std

Colormap min scale for std map. Default: 0

--cMax_std

Colormap max scale for std map. Default: automatic

--plottingFileExtension

By default: png. Other options: svg, pdf, png

--shuffle

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

--cmap

Colormap. Default: coolwarm

--cmap_std

Colormap for std map. Default: coolwarm

--N_bootstrap

Number of bootstrapping cycles. Default=9999

Example

plot_bootstrapping --input Trace_Trace_all_ROIs_filtered_beta_mask0_exp_ND_1_PDX1LR_Matrix_PWDscMatrix.npy -U Trace_Trace_all_ROIs_filtered_exocrine_mask0_exp_ND_3_PDX1LR_Matrix_uniqueBarcodes.ecsv --N_bootstrap 100