transposonmapper.plotting
transposonmapper.plotting¶
- transposonmapper.plotting.dna_features_plot(chrom, dna_df2, roi_start, roi_end, len_chr, plotting, variable)[source]¶
Plot function for the genomic features per chromosome
- Parameters
chrom (str) –
Region: e.g. chromosome number (either a normal number between 1 and 16 or in roman numerals between I and XVI),
a list like [‘V’, 0, 14790] which creates a barplot between basepair 0 and 14790) or a genename.
dna_df2 (pandas.dataframe) – Dataframe containing information about the selected chromosome
roi_start (int) – The start of the chromosome roi_start,roi_end,region_type,chrom=input_region(region=region,verbose=verbose)
roi_end (int) – The end of the chromosome roi_start,roi_end,region_type,chrom=input_region(region=region,verbose=verbose)
len_chr ([type]) – Length of the chromosome dna_dict,start_chr,end_chr,len_chr,feature_orf_dict=gene_location(chrom,gene_position_dict,verbose)
plotting (optional) – default True
variable (optional) – default “reads”
- transposonmapper.plotting.profile_genome_plot(bar_width, l_genome, allinsertionsites_list, allcounts_binnedlist, summed_chr_length_dict, middle_chr_position, chrom_list, variable, genes_currentchrom_pos_list, gene_pos_dict)[source]¶
Plot function to show the whole insertion map throughout the genome
- Parameters
bar_width (int) – The width for the histogram of the plot, by default None , which means internally the length of the genome over 1000
l_genome (int) – The length of the genome in bp
allinsertionsites_list (list) – List of insertions sites
allcounts_binnedlist (list) – List of binned counts
summed_chr_length_dict (dict) – The cumulative sum of the length of every chromosome
middle_chr_position (dict) – Middle chromosome position per chromosome
chrom_list (list) – A list of all the chromosomes
variable (str) – It could be “transposons” or “reads”
genes_currentchrom_pos_list (list) – List of genes per chromosome
gene_pos_dict (dict) – Postion along the genome of every gene