Michael Paulini epaule
pgonzale60
/ busco_to_synteny_plot.R
Last active
August 25, 2022 13:07
Take in two BUSCO full table and generate a dot plot of colinearity from hits in long sequences
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| library(tidyverse) | |
| library(scales) | |
| library(gtools) | |
| min_seq_size <- 5e5 # Sequences shorter than this will not be plotted (the size of the sequence is inferred from the maximum coordinate of a BUSCO) | |
| ref_busco <- "~/Downloads/CABPSW02.yahs_scaffolds_final_nematoda_odb10_full_table.tsv" # path to reference file | |
| query_busco <- "~/Downloads/APS7_sophie.v4_nopipe.fasta.yahs_scaffolds_final_nematoda_odb10_full_table.tsv" # path to query file | |
| ref_species <- "A. rhodensis" # text in x axis of plot | |
| query_species <- "A. freiburgensis" # text in y axis of plot |
pgonzale60
/ multispecies_oxford_plot.R
Last active
August 25, 2022 13:10
Compares oxford plots of multiple species using shared coordinates rather than facets. Designed for BUSCO's full table.
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| library(tidyverse) | |
| # User input #### | |
| x_species <- c("nxOscDolc1.1", "nxOscOnir1.2") | |
| y_species <- c("nxOscSper1.1", "nxOscSpeu1.1") | |
| # path to BUSCO table directory | |
| # path must end in "/" (e.g. busco_dir/) | |
| busco_dir <- "analyses/paper1/prelim_to_20220220/nemaChromQC/" |