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updated docs for the logo functions and tested all of them again

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Tanushree Tunstall 2022-01-26 15:53:53 +00:00
parent 2f7f40efb1
commit 7317156bba
5 changed files with 135 additions and 80 deletions
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84
scripts/functions/tests/test_logo_plots.R
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@ -12,29 +12,29 @@ source("~/git/LSHTM_analysis/scripts/plotting/get_plotting_dfs.R")
# mainly OR
# script: logoP_or.R
################################
# LogoPlotCustomH (plot_df = merged_df3
# , x_axis_colname = "position"
# , y_axis_colname = "or_mychisq"
# , symbol_colname = "mutant_type"
# , y_axis_log = T
# , log_value = log10
# , y_axis_increment = 100
# , rm_empty_y = T
# , my_logo_col = 'chemistry'
# , x_lab = "Wild-type position"
# , y_lab = "Odds Ratio"
# , x_ats = 10 # text size
# , x_tangle = 90 # text angle
# , y_ats = 22
# , y_tangle = 0
# , x_tts = 19 # title size
# , y_tts = 22
# #, leg_pos = c(0.05,-0.12)
# , leg_pos = "top"
# , leg_dir = "horizontal"
# , leg_ts = 15 # leg text size
# , leg_tts = 16 # leg title size
# )
LogoPlotCustomH (plot_df = merged_df3
, x_axis_colname = "position"
, y_axis_colname = "or_mychisq"
, symbol_colname = "mutant_type"
, y_axis_log = T
, log_value = log10
, y_axis_increment = 100
, rm_empty_y = T
, my_logo_col = 'chemistry'
, x_lab = "Wild-type position"
, y_lab = "Odds Ratio"
, x_ats = 10 # text size
, x_tangle = 90 # text angle
, y_ats = 22
, y_tangle = 0
, x_tts = 19 # title size
, y_tts = 22
#, leg_pos = c(0.05,-0.12)
, leg_pos = "top"
, leg_dir = "horizontal"
, leg_ts = 15 # leg text size
, leg_tts = 16 # leg title size
)
########################################
@ -42,25 +42,25 @@ source("~/git/LSHTM_analysis/scripts/plotting/get_plotting_dfs.R")
# wild-type and mutant aa
# script: logoP_snp.R
########################################
# 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.
# , my_logo_col = "chemistry"
# , x_lab = "Wild-type position"
# , y_lab = "nsSNP count"
# , x_ats = 10 # text size
# , x_tangle = 90 # text angle
# , y_ats = 18
# , y_tangle = 0
# , x_tts = 18 # title size
# , y_tts = 18
# , leg_pos = "top" # can be top, left, right and bottom or c(0.8, 0.9)
# , leg_dir = "horizontal" # can be vertical or horizontal
# , leg_ts = 14 # leg text size
# , leg_tts = 16 # leg title size
# )
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.
, my_logo_col = "chemistry"
, x_lab = "Wild-type position"
, y_lab = "nsSNP count"
, x_ats = 10 # text size
, x_tangle = 90 # text angle
, y_ats = 18
, y_tangle = 0
, x_tts = 18 # title size
, y_tts = 18
, leg_pos = "top" # can be top, left, right and bottom or c(0.8, 0.9)
, leg_dir = "horizontal" # can be vertical or horizontal
, leg_ts = 14 # leg text size
, leg_tts = 16 # leg title size
)
####################################################
# Logo plot MSA