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 BARCODES] [-O OUTPUT]
                          [--fontsize FONTSIZE] [--axisLabel] [--c_min CMIN]
                          [--c_max CMAX] [--c_min_std CMIN_STD]
                          [--c_max_std CMAX_STD]
                          [--output_format {png,svg,pdf}] [--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, --barcodes, --uniqueBarcodes

csv file with list of unique barcodes

-O, --output, --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

--c_min, --cMin

Colormap min scale. Default: 0

--c_max, --cMax

Colormap max scale. Default: automatic

--c_min_std, --cMin_std

Colormap min scale for std map. Default: 0

--c_max_std, --cMax_std

Colormap max scale for std map. Default: automatic

--output_format

Possible choices: png, svg, pdf

Output image format. Default = png.

Default: 'png'

--shuffle

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

--cmap, --c_map

Colormap. Default: coolwarm

--cmap_std

Colormap for std map. Default: coolwarm

--N_bootstrap

Number of bootstrapping cycles. Default=9999

Output Files

The script generates:

1. [output]/Fig_[matrixfile]bootstrapping_median.npy: Bootstrapped median matrix values.

2. [output]/Fig_[matrixfile]bootstrapping_median.[format]: Heatmap of the bootstrapped median matrix.

3. [output]/Fig_[matrixfile]bootstrapping_std_median.npy: Standard-error matrix values from bootstrapping.

4. [output]/Fig_[matrixfile]bootstrapping_std_median.[format]: Heatmap of the standard-error matrix.

Examples

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

Notes

• See the command-line reference above for the complete option list.