tanu/LSHTM_analysis
1
0
Fork 0
Code Issues Pull requests Releases Wiki Activity

modified ks test to output all stats needed in one script

Browse source
This commit is contained in:
Tanushree Tunstall 2022-08-12 14:35:03 +01:00
parent 22be845e1f
commit f5f1e388c3
3 changed files with 309 additions and 106 deletions
Download patch file Download diff file Expand all files Collapse all files

3
scripts/plotting/plotting_thesis/corr_plots_thesis.R
View file

@ -321,14 +321,13 @@ svg('/tmp/foo.svg', width=10, height=10, )
corr_plotting_df = corr_df_ps
ggpairs(corr_plotting_df, columns = 1:(ncol(corr_plotting_df)-corr_end)
ggpairs(corr_plotting_df, columns = 1:(ncol(corr_plotting_df)-1)
, upper = list(continuous = wrap('cor', method = "spearman"))
, aes(colour = factor(dst_mode), alpha = 0.5)
, title="correlogram with ggpairs()") +
scale_colour_manual(values = c("red", "blue")) +
scale_fill_manual(values = c("red", "blue"))
dev.off()

11
scripts/plotting/plotting_thesis/stats/embb_ks_lineage_all_comp.csv Normal file
View file

@ -0,0 +1,11 @@
"comparison","method","ks_statistic","ks_pvalue","n_samples","n_samples_total","pvalue_signif","ks_comp_type","gene_name"
"L1 vs L2","Two-sample Kolmogorov-Smirnov test",0.562081297123684,0,"L1(4013), L2(3554)",7567,"****","between_lineages","embb"
"L1 vs L3","Two-sample Kolmogorov-Smirnov test",0.521960420540757,0,"L1(4013), L3(692)",4705,"****","between_lineages","embb"
"L1 vs L4","Two-sample Kolmogorov-Smirnov test",0.414409376879199,0,"L1(4013), L4(5276)",9289,"****","between_lineages","embb"
"L2 vs L3","Two-sample Kolmogorov-Smirnov test",0.191637851675715,0,"L2(3554), L3(692)",4246,"****","between_lineages","embb"
"L2 vs L4","Two-sample Kolmogorov-Smirnov test",0.177978192411417,0,"L2(3554), L4(5276)",8830,"****","between_lineages","embb"
"L3 vs L4","Two-sample Kolmogorov-Smirnov test",0.110182657206589,7.08096017931759e-07,"L3(692), L4(5276)",5968,"****","between_lineages","embb"
"overall R vs S distributions","Two-sample Kolmogorov-Smirnov test",0.549577339308325,0,"R(n=6878) S(n=6657)",13535,"****","between_lineages","embb"
"L1: R vs S","Two-sample Kolmogorov-Smirnov test",0.654874747810162,0,"R(n=209), S(n=3804)",4013,"****","within_lineages","embb"
"L2: R vs S","Two-sample Kolmogorov-Smirnov test",0.368060163680602,0,"R(n=3014), S(n=540)",3554,"****","within_lineages","embb"
"L3: R vs S","Two-sample Kolmogorov-Smirnov test",0.473750449478605,0,"R(n=486), S(n=206)",692,"****","within_lineages","embb"
1 comparison method ks_statistic ks_pvalue n_samples n_samples_total pvalue_signif ks_comp_type gene_name
2 L1 vs L2 Two-sample Kolmogorov-Smirnov test 0.562081297123684 0 L1(4013), L2(3554) 7567 **** between_lineages embb
3 L1 vs L3 Two-sample Kolmogorov-Smirnov test 0.521960420540757 0 L1(4013), L3(692) 4705 **** between_lineages embb
4 L1 vs L4 Two-sample Kolmogorov-Smirnov test 0.414409376879199 0 L1(4013), L4(5276) 9289 **** between_lineages embb
5 L2 vs L3 Two-sample Kolmogorov-Smirnov test 0.191637851675715 0 L2(3554), L3(692) 4246 **** between_lineages embb
6 L2 vs L4 Two-sample Kolmogorov-Smirnov test 0.177978192411417 0 L2(3554), L4(5276) 8830 **** between_lineages embb
7 L3 vs L4 Two-sample Kolmogorov-Smirnov test 0.110182657206589 7.08096017931759e-07 L3(692), L4(5276) 5968 **** between_lineages embb
8 overall R vs S distributions Two-sample Kolmogorov-Smirnov test 0.549577339308325 0 R(n=6878) S(n=6657) 13535 **** between_lineages embb
9 L1: R vs S Two-sample Kolmogorov-Smirnov test 0.654874747810162 0 R(n=209), S(n=3804) 4013 **** within_lineages embb
10 L2: R vs S Two-sample Kolmogorov-Smirnov test 0.368060163680602 0 R(n=3014), S(n=540) 3554 **** within_lineages embb
11 L3: R vs S Two-sample Kolmogorov-Smirnov test 0.473750449478605 0 R(n=486), S(n=206) 692 **** within_lineages embb