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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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58
scripts/functions/logoP_or.R
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@ -1,46 +1,52 @@
#logo plots
# Input:
# Data:
# plot_df: merged_df3 containing the OR column to use as y-axis or any other relevant column
# create functions
# x_axis_colname = "position"
# y_axis_colname = "or_mychisq"
# symbol_colname = "mutant_type"
# y_axis_log = F
# log_value = log10
# if used, y-axis label has "Log" appended to it
# one with OR
# --> select/drop down option to remove empty positions
# --> select/drop down option for colour
# --> if clustalx and taylor, set variable to black bg + white font
# --> if chemistry and hydrophobicity, then grey bg + black font
# my_logo_col = c("chemistry", "hydrophobicity", "clustalx", "taylor")
# --> if clustalx and taylor, set variable to black bg + white font
# --> if chemistry and hydrophobicity, then grey bg + black font
# --> select/drop down option for log scale
# --> should include WT
# rm_empty_y = F
# option to remove empty positions i.e positions with no assocaited y-val
# one for multiple muts
# --> select/drop down option to filter count of nsSNPs
# --> select/drop down option for colour
# --> should include WT
# y_axis_log = F
# option to use log scale
# FIXME Minor bug: if used with rm_empty_y, sometimes the labels are too small to render(!?)
# so positions appear empty despite having y-vals
# ...other params
# Returns: Logo plot from combined data containing specific y-value such as OR, etc by position.
# TODO: SHINY
# select/drop down option to remove empty positions
# select/drop down option for colour
# select/drop down option for log scale
# include WT
# Make it hover over position and then get the corresponding data table!
#%%======================================================================
########################a###########################################################
#==================
# logo data: OR
#==================
# NOTE: my_logo_col
# Can be one of these: 'chemistry', 'hydrophobicity', 'clustalx', 'taylor'
# if 'chemistry' or 'hydrophobicity' --> then bg is grey with black font (x, y and labels)
# if 'clustalx'or 'taylor' --> then bg is black with white font (x, y and labels)
#, theme_bgc =
#, xfont_bgc =
#, yfont_bgc =
#, xtt_col =
#, ytt_col =
LogoPlotCustomH <- function(plot_df
, x_axis_colname = "position"
, y_axis_colname = "or_mychisq"
, symbol_colname = "mutant_type"
, my_logo_col = "chemistry"
, rm_empty_y = F
, y_axis_log = F
, log_value = log10
, y_axis_increment = 5
, rm_empty_y = F
, my_logo_col = "chemistry"
, x_lab = "Position"
, y_lab = "Odds Ratio"
, x_ats = 12 # text size