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

scripts/functions/ed_pfm_data.R

@@ -1,4 +1,3 @@
-library(Logolas)
 source("~/git/LSHTM_analysis/scripts/functions/my_logolas.R")
 #####################################################################################
 # DataED_PFM(): 

scripts/functions/logoP_msa.R

@@ -1,8 +1,46 @@
+#####################################################################################
+# LogoPlotMSA(): 
+# Input:
+  # Data:
+    # msaSeq_mut: MSA chr vector for muts
+    # msaSeq_wt: MSA chr vector for wt
+
+  # Logo type params:
+  # logo_type = c("EDLogo", "bits_pfm", "probability_pfm", "bits_raw", "probability_raw")
+    # EDLogo: calculated from the Logolas package based on PFM matrix (scaled). 
+        #The required content from the package is sourced locally within 'my_logolas.R'
+    # bits_pfm: Information Content based on PFM scaled matrix (my_logolas.R)
+    # probability_pfm: Probability based on PFM scaled matrix (my_logolas.R)
+    # bits_raw: Information Content based on Raw MSA (ggseqlogo)
+    # probability_raw: Probability based on Raw MSA (ggseqlogo)
+  
+  # EDScore_type = c("log", log-odds", "diff", "probKL", "ratio", "unscaled_log", "wKL")
+  # bg_prob: background probability, default is equal i.e NULL.
+    # This is used by the internal call to DataED_PFM(). This func takes thse args. I have used it here for
+    # completeness and allow nuanced plot control
+  
+  # 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 
+
+  # ...other params
+
+# Returns: Logo plots from MSA both mutant and wt (for comparability)
+# For my case, I always use it as it helps see what is at the wild-type already!
+
+# TODO: SHINY
+# drop down: logo_type
+# drop down: ED score type
+# drop down/enter field : bg probability (in the actual plot function!)
+# drop down: my_logo_col
+# Make it hover over position and then get the corresponding data table!
+###################################################################################
+
+
 ###########################################
 LogoPlotMSA <- function(msaSeq_mut # chr vector
                         , msaSeq_wt # chr vector
-                        #, msa_method = c("custom") # can be "bits", "probability" or "custom"
+                        , logo_type = c("EDLogo") #"bits_pfm", "probability_pfm", "bits_raw", "probability_raw")
-                        , logo_type = c("EDLogo") #"bits_pfm", "probability_pfm", "bits_raw", "probability_raw") # can be "bits", "probability" or "custom"
                         , EDScore_type =  c("log") # see if this relevant, or source function should have it!
                         , bg_prob = NULL
                         , my_logo_col = "chemistry" 

scripts/functions/logoP_or.R

@@ -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
+# my_logo_col = c("chemistry", "hydrophobicity", "clustalx", "taylor")
-  # --> select/drop down option to remove empty positions
+  # --> if clustalx and taylor,  set variable to black bg + white font
-  # --> select/drop down option for colour
+  # --> if chemistry and hydrophobicity, then grey bg +  black font 
-      # --> 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
+# rm_empty_y = F
-  # --> should include WT
+  # option to remove empty positions i.e positions with no assocaited y-val 
 
-# one for multiple muts
+# y_axis_log  = F
-  # --> select/drop down option to filter count of nsSNPs
+  # option to use log scale 
-  # --> select/drop down  option for colour
+  # FIXME Minor bug: if used with rm_empty_y, sometimes the labels are too small to render(!?)
-  # --> should include WT
+    # 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

scripts/functions/logoP_snp.R

@@ -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
+# x_axis_colname = "position"
-  # --> select/drop down option to filter count of nsSNPs
+# symbol_mut_colname = "mutant_type"
-  # --> select/drop down  option for colour
+# symbol_wt_colname = "mutant_type"
-  # --> should include WT
+# 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
+# ...other params
-#tab_wt # wt logo plot
+
+# 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

scripts/functions/tests/test_logo_plots.R

@@ -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
+LogoPlotCustomH (plot_df = merged_df3
-#                             , x_axis_colname = "position"
+                            , x_axis_colname = "position"
-#                             , y_axis_colname = "or_mychisq"
+                            , y_axis_colname = "or_mychisq"
-#                             , symbol_colname = "mutant_type"
+                            , symbol_colname = "mutant_type"
-#                             , y_axis_log  = T
+                            , y_axis_log  = T
-#                             , log_value = log10
+                            , log_value = log10
-#                             , y_axis_increment = 100
+                            , y_axis_increment = 100
-#                             , rm_empty_y = T
+                            , rm_empty_y = T
-#                             , my_logo_col = 'chemistry'
+                            , my_logo_col = 'chemistry'
-#                             , x_lab = "Wild-type position"
+                            , x_lab = "Wild-type position"
-#                             , y_lab = "Odds Ratio"
+                            , y_lab = "Odds Ratio"
-#                             , x_ats = 10 # text size
+                            , x_ats = 10 # text size
-#                             , x_tangle = 90 # text angle
+                            , x_tangle = 90 # text angle
-#                             , y_ats = 22
+                            , y_ats = 22
-#                             , y_tangle = 0
+                            , y_tangle = 0
-#                             , x_tts = 19 # title size
+                            , x_tts = 19 # title size
-#                             , y_tts = 22
+                            , y_tts = 22
-#                             #, leg_pos = c(0.05,-0.12)
+                            #, leg_pos = c(0.05,-0.12)
-#                             , leg_pos = "top"
+                            , leg_pos = "top"
-#                             , leg_dir = "horizontal"
+                            , leg_dir = "horizontal"
-#                             , leg_ts = 15 # leg text size
+                            , leg_ts = 15 # leg text size
-#                             , leg_tts = 16 # leg title 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
+LogoPlotSnps(plot_df = merged_df3
-#              , x_axis_colname = "position"
+             , x_axis_colname = "position"
-#              , symbol_mut_colname = "mutant_type"
+             , symbol_mut_colname = "mutant_type"
-#              , symbol_wt_colname = "wild_type"
+             , symbol_wt_colname = "wild_type"
-#              , omit_snp_count = c(1)# can be 0,1, 2, etc.
+             , omit_snp_count = c(1)# can be 0,1, 2, etc.
-#              , my_logo_col = "chemistry"
+             , my_logo_col = "chemistry"
-#              , x_lab = "Wild-type position"
+             , x_lab = "Wild-type position"
-#              , y_lab = "nsSNP count"
+             , y_lab = "nsSNP count"
-#              , x_ats = 10 # text size
+             , x_ats = 10 # text size
-#              , x_tangle = 90 # text angle
+             , x_tangle = 90 # text angle
-#              , y_ats = 18
+             , y_ats = 18
-#              , y_tangle = 0
+             , y_tangle = 0
-#              , x_tts = 18 # title size
+             , x_tts = 18 # title size
-#              , y_tts = 18
+             , y_tts = 18
-#              , leg_pos = "top" # can be top, left, right and bottom or c(0.8, 0.9)
+             , 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_dir = "horizontal" # can be vertical or horizontal
-#              , leg_ts = 14 # leg text size
+             , leg_ts = 14 # leg text size
-#              , leg_tts = 16 # leg title size
+             , leg_tts = 16 # leg title size
-# )
+)
 
 ####################################################
 # Logo plot MSA