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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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30
scripts/functions/logoP_snp.R
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@ -1,17 +1,29 @@
#logo plots
########################a###########################################################
# Input:
# Data
# plot_df: merged_df3 containing the OR column to use as y-axis or any other relevant column
# one for multiple muts
# --> select/drop down option to filter count of nsSNPs
# --> select/drop down option for colour
# --> should include WT
# x_axis_colname = "position"
# symbol_mut_colname = "mutant_type"
# symbol_wt_colname = "mutant_type"
# omit_snp_count = c(0, 1, 2...) can be used to filter positions with specified snp count
# Data used
# 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
#tab_mt # mutant logo plot
#tab_wt # wt logo plot
# ...other params
# Returns: Logo plot from combined data containing all nsSNPs per position.
# Helps to see the overview of SNP diversity
# TODO: SHINY
# select/drop down: omit_snp_count
# select/drop down: my_logo_col
# should include WT??
# Make it hover over position and then get the corresponding data table!
#%%======================================================================
####################################################################################
#==================
# logo data: OR