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This commit is contained in:
Tanushree Tunstall 2022-03-02 11:44:04 +00:00
parent 2274f01f23
commit 6c6709e41e
6 changed files with 198 additions and 29 deletions
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17
scripts/functions/tests/test_logo_plots.R
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@ -16,10 +16,10 @@ LP1<- LogoPlotCustomH (plot_df = merged_df3
, x_axis_colname = "position"
, y_axis_colname = "or_mychisq"
, symbol_colname = "mutant_type"
, y_axis_log = T
, y_axis_log = F
, log_value = log10
, y_axis_increment = 100
, rm_empty_y = T
, y_axis_increment = 50
, rm_empty_y = F
, my_logo_col = 'chemistry'
, x_lab = "Wild-type position"
, y_lab = "Odds Ratio"
@ -45,7 +45,7 @@ LP2<- LogoPlotSnps(plot_df = merged_df3
, x_axis_colname = "position"
, symbol_mut_colname = "mutant_type"
, symbol_wt_colname = "wild_type"
, omit_snp_count = c(1)# can be 0,1, 2, etc.# DD
, omit_snp_count = c(0)# can be 0,1, 2, etc.# DD
, my_logo_col = "chemistry" #DD
, x_lab = "Wild-type position"
, y_lab = "nsSNP count"
@ -75,8 +75,9 @@ LP2<- LogoPlotSnps(plot_df = merged_df3
# to select a small dataset: see test_ed_pfm_data.R
#####################################################
LP3<- LogoPlotMSA(msaSeq_mut = msa_seq
, msaSeq_wt = wt_seq
LP3<- LogoPlotMSA(unified_msa
#msaSeq_mut = msa_seq
#, msaSeq_wt = wt_seq
, logo_type = c("EDLogo") # "EDLogo", bits_pfm", "probability_pfm", "bits_raw", "probability_raw")
, EDScore_type = c("log")
, bg_prob = NULL
@ -90,7 +91,7 @@ LP3<- LogoPlotMSA(msaSeq_mut = msa_seq
#, y_lab_mut
, x_ats = 10
, x_tangle = 90
, y_ats = 15
, y_ats = 12
, y_tangle = 0
, x_tts = 13
, y_tts = 13
@ -106,7 +107,7 @@ out_logoP = cowplot::plot_grid(LP3, LP1, LP2
, nrow = 3
, ncol = 1
, rel_width = c(1/3, 0.5/3, 1/3)
, rel_heights = c(1, 1, 1)
, rel_heights = c(0.8/2, 0.5/2, 0.7/2)
, align = "hv")
out_logoP