dotools_py.pl.split_bar_gsea

dotools_py.pl.split_bar_gsea(df, term_col, col_split, cond_col, pos_cond, cutoff=40, log10_transform=True, figsize=(12, 8), topn=10, colors_pairs=('sandybrown', 'royalblue'), alpha_colors=0.3, path=None, spacing=5, txt_size=12, filename='SplitBar.svg', title='Top 10 GO Terms in each Condition', show=True)

Split BarPlot for GO terms.

This function generates a split barplot. This is a plot where the top 10 GO terms are shown, sorted based on a column col_split. Two conditions are shown at the same time. One condition is shown in the positive axis, while the other in the negative one. The condition to be shown as positive is set with pos_col.

Warning

Expected a filtered dataframe containing only significant Terms

Parameters:

df DataFrame

dataframe with the results of a gene set enrichment analysis.

term_col str

column in the dataframe that contains the terms.

col_split str

column in the dataframe that will be used to sort and split the plot.

cond_col str

column in the dataframe that contains the condition information.

pos_cond str

condition that will be shown in the positive side of the plot.

cutoff int (default: 40)

maximum number of characters per line.

log10_transform bool (default: True)

if col_split contains values between 0 and 1, assume they are pvals and apply a -log10 transformation.

figsize tuple[int, int] (default: (12, 8))

figure size.

topn float (default: 10)

how many terms are shown.

path str | PathLike[str] | Path (default: None)

path to save the plot.

filename str (default: 'SplitBar.svg')

filename for the plot.

spacing float (default: 5)

space to add between bars and origin. It is a percentage value, indicating that the bars start at 5 % of the maximum X axis value.

txt_size float (default: 12)

size of the go terms text.

alpha_colors float (default: 0.3)

alpha value for the colors of the bars.

colors_pairs list (default: ('sandybrown', 'royalblue'))

colors for each condition (1st color –> negative axis; 2nd color –> positive axis).

title str (default: 'Top 10 GO Terms in each Condition')

title of the plot.

show bool (default: True)

if False, the axis is return.

Return type:

Axes | None

Returns:

Depending on show, returns the plot if set to True or a dictionary with the axes.

Example

import dotools_py as do
adata = do.dt.example_10x_processed()
do.tl.rank_genes_groups(adata,  'condition', method='wilcoxon', tie_correct=True, pts=True)
table = do.get.dge_results(adata)
table = table[table.group == 'disease']
table_go = do.tl.go_analysis(table, 'GeneName', 'padj', 'log2fc', specie='Human', go_catgs = ['GO_Molecular_Function_2023', 'GO_Cellular_Component_2023', 'GO_Biological_Process_2023'])
table_go = table_go[table_go['P-value'] < 0.25]
do.pl.split_bar_gsea(table_go, 'Term', 'Combined Score', 'state', 'enriched', show=True)