hic3defdr.plotting.grid module¶
-
hic3defdr.plotting.grid.
plot_grid
(i, j, w, row, col, raw, scaled, mu_hat_alt, mu_hat_null, qvalues, disp_idx, loop_idx, design, fdr, cluster_size, vmax=100, fdr_vmid=0.05, color_cycle=('blue', 'green', 'purple', 'yellow', 'cyan', 'red'), despine=False, **kwargs)[source]¶ Plots a combination visualization grid focusing on a specific pixel on a specific chromosome, combining heatmaps, cluster outlines, and stripplots.
Parameters: - j (i,) – The row and column index of the pixel to focus on.
- w (int) – The size of the heatmap will be
2*w + 1
bins in each dimension. - col (row,) – The row and column indices corresponding to the rows of the
raw
andscaled
matrices. - scaled (raw,) – The raw and scaled data for each pixel (rows) and each replicate (columns).
- mu_hat_null (mu_hat_alt,) – The estimated mean parameter under the alternate and null model,
respectively. First dimension is pixels for which dispersion was
estimated, whose row and column coordinates in the complete square
matrix are given by
row[disp_idx]
andcol[disp_idx]
, respectively. Columns ofmu_hat_alt
correspond to conditions, whilemu_hat_null
has no second dimension. - qvalues (np.ndarray) – Vector of q-values called per pixel whose dispersion was estimated and
which lies in a loop. The row and column coordinates in the complete
square matrix are given by
row[disp_idx][loop_idx]
andcol[disp_idx][loop_idx]
, respectively. - disp_idx (np.ndarray) – Boolean matrix indicating which pixels in
zip(row, col)
had their dispersion estimated. - loop_idx (np.ndarray) – Boolean matrix indicating which pixels in
zip(row[disp_idx], col[disp_idx])
lie within loops. - design (pd.DataFrame) – Pass a DataFrame with boolean dtype whose rows correspond to replicates and whose columns correspond to conditions. Replicate and condition names will be inferred from the row and column labels, respectively.
- fdr (float) – The FDR threshold to use when outlining clusters.
- cluster_size (int) – The cluster size threshold to use when outlining clusters.
- vmax (float) – The maximum of the colorscale to use when plotting normalized heatmaps.
- fdr_vmid (float) – The FDR value at the middle of the colorscale used for plotting the q-value heatmap.
- color_cycle (list of matplotlib colors) – The color cycle to use over conditions.
- kwargs (kwargs) – Typical plotter kwargs.
Returns: The first pyplot axis returned is injected by
@plotter
. The grid of pyplot axes is the second return value from the call toplt.subplots()
that is used to create the grid. The function takes two args, an FDR and a cluster size, and redraws the cluster outlines using the new parameters.Return type: pyplot axis, grid of pyplot axes, function