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added both test logo plots in one script

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This commit is contained in:
Tanushree Tunstall 2022-01-16 15:00:54 +00:00
parent efe6703673
commit 07aedfe286
3 changed files with 58 additions and 51 deletions
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27
scripts/functions/tests/test_logoP.R
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@ -1,27 +0,0 @@
#source("~/git/LSHTM_analysis/config/gid.R")
#source("~/git/LSHTM_analysis/scripts/plotting/get_plotting_dfs.R")
LogoPlotCustomH (plot_df = merged_df3
, x_axis_colname = "position"
, y_axis_colname = "or_mychisq"
, symbol_colname = "mutant_type"
, y_axis_log = F
, log_value = log10
, y_axis_increment = 5
, rm_empty_y = T
, my_logo_col = 'chemistry'
, x_lab = "Position"
, y_lab = "Odds Ratio"
, x_ats = 12 # 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
)

24
scripts/functions/tests/test_logoP_snp.R
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@ -1,24 +0,0 @@
#source("~/git/LSHTM_analysis/config/gid.R")
#source("~/git/LSHTM_analysis/scripts/plotting/get_plotting_dfs.R")
LogoPlotSnps(plot_df = merged_df3
, x_axis_colname = "position"
, symbol_mut_colname = "mutant_type"
, symbol_wt_colname = "wild_type"
, omit_snp_count = c(0)# can be 1, 2, etc.
, my_logo_col = "taylor"
, x_lab = "Wild-type position"
, y_lab = ""
, x_ats = 13 # text size
, x_tangle = 90 # text angle
, y_ats = 20
, 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
)

58
scripts/functions/tests/test_logo_plots.R Normal file
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source("~/git/LSHTM_analysis/config/gid.R")
source("~/git/LSHTM_analysis/scripts/plotting/get_plotting_dfs.R")
################################
# Logo plot with custom Y axis
# mainly OR
# script: logoP.R
################################
LogoPlotCustomH (plot_df = merged_df3
, x_axis_colname = "position"
, y_axis_colname = "or_mychisq"
, symbol_colname = "mutant_type"
, y_axis_log = F
, log_value = log10
, y_axis_increment = 5
, rm_empty_y = F
, my_logo_col = 'chemistry'
, x_lab = "Wild-type position"
, y_lab = "Odds Ratio"
, x_ats = 12 # 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
)
########################################
# Logo plot showing nsSNPs by positions
# 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(0)# can be 1, 2, etc.
, my_logo_col = "chemistry"
, x_lab = "Wild-type position"
, y_lab = ""
, x_ats = 13 # text size
, x_tangle = 90 # text angle
, y_ats = 20
, 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
)