1. Giovanni Marco Dall'Olio
  2. genotype_space

Commits

Author Commit Message Date Builds
Giovanni Marco Dall'Olio
CLEAN: removing pathway analysis results
Giovanni Marco Dall'Olio
CLEAN: removed archive folder, to reduce repo size
Giovanni Marco Dall'Olio
DOCS: updated project name and reference
Giovanni Marco Dall'Olio
CODING: removed label from coding/noncoding plots. The global population is in the second-to-last page
Giovanni Marco Dall'Olio
SAMPLE_SIZE: better facet titles, and removed global title, for publication
Giovanni Marco Dall'Olio
SIMS: using two-sided alternative hypothesis; improved plots
Giovanni Marco Dall'Olio
CORR: obtaining the p-values, and moving the position of the R coefficient in the figure
Giovanni Marco Dall'Olio
SAMPLE_SIZE: updated axis to include 300 and 100
Giovanni Marco Dall'Olio
SIMS: added script to calculate qqplots, wilcoxon, kolmogorov-smirnov of neutral vs sele simulations
Giovanni Marco Dall'Olio
SIMS: quick&dirty script to compare neutral and selection simulations
Giovanni Marco Dall'Olio
BEST: calculated a new property, largest component (n.vertices/n.components)
Giovanni Marco Dall'Olio
BEST: obtained a table of all the top scores, after filtering low quality regions
Giovanni Marco Dall'Olio
UCSC: downloaded table of known Genes from UCSC hg19
Giovanni Marco Dall'Olio
BEST: wrote a script to merge all the neighbor regions in the top scores, and create a bed file
Giovanni Marco Dall'Olio
BEST: extracted the best scores
Giovanni Marco Dall'Olio
BEST: increasing cutoffs
Giovanni Marco Dall'Olio
BEST: disabling calculation of quantiles. Calculating an average per window of 11 SNPs
Giovanni Marco Dall'Olio
BEST: added option to parse only global_noAMR pop Rscript src/get_topscores_byproperty.R --debug --only_global
Giovanni Marco Dall'Olio
SIMS: reducing image size
Giovanni Marco Dall'Olio
CODING: removed av_closeness Rscript src/plot_chromosome_correlations.R
Giovanni Marco Dall'Olio
CODING: removing av_closenes Rscript src/plot_boxplotsBySNPAnnotation_onepageperproperty.R --plot_type pointrange --globa
Giovanni Marco Dall'Olio
SIMS: removing av_closeness from the plot Rscript src/plot_simulations_NeutralVsSelection.R --plot_type barcharts
Giovanni Marco Dall'Olio
SAMPLE: removing av_closeness
Giovanni Marco Dall'Olio
WINDOW: removing av_closeness from window plot Rscript src/plot_networkproperties_bywindowsize.R -r results/tables/whole_chromosomes/multiple_windows/ -o results/plots/window_size/networkproperties_bywindowsize_chr22_onlypops.pdf -b 30 -s -t "Chromosome 22" -n "glob"
Giovanni Marco Dall'Olio
SAMPLE: SIMS: correct label for simulation plots Rscript src/plot_networkproperties_bysamplesize.R -r data/simulations_5000/background/by_samplesize/w11/ -n glob -s -o results/plots/sample_size/networkproperties_bysamplesize_sims_5000.pdf --plot_type linerange_r -t "Simulations"
Giovanni Marco Dall'Olio
SAMPLE: SIMS: For the simulations, I have decided to plot the X axis in the reverse order Rscript src/plot_networkproperties_bysamplesize.R -r data/simulations_5000/background/by_samplesize/w11/ -n glob -s -o results/plots/sample_size/networkproperties_bysamplesize_sims_5000.pdf --plot_type linerange_r
Giovanni Marco Dall'Olio
CODING: removed the p-value labels in the pointrange plots Rscript src/plot_boxplotsBySNPAnnotation_onepageperproperty.R --plot_type pointrange --global
Giovanni Marco Dall'Olio
DOCS: added a description of all the network properties implemented (former Supplementary Table S1)
Giovanni Marco Dall'Olio
CYTOSCAPE: version of the figures used in the thesis
Giovanni Marco Dall'Olio
TEST_LOGS: running tests, after leaving this work aside for a few months (thesis writing)
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