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updated docs for dm_om_data.R

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Tanushree Tunstall 2022-02-01 16:23:03 +00:00
parent e795c00831
commit 3d45780c1a
4 changed files with 54 additions and 179 deletions
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50
scripts/plotting/get_plotting_dfs.R
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@ -88,13 +88,6 @@ merged_df3 = all_plot_dfs[[2]]
merged_df2_comp = all_plot_dfs[[3]]
merged_df3_comp = all_plot_dfs[[4]]
#======================================================================
####################################################################
# Data for combining other dfs
####################################################################
#source("other_dfs_data.R")
# Fixed this at source i.e python script
# Moved: "other_dfs_data.R" to redundant/
####################################################################
# Data for subcols barplot (~heatmap)
@ -109,35 +102,39 @@ merged_df3_comp = all_plot_dfs[[4]]
# Data for logoplots
####################################################################
#source(paste0(plot_script_path, "logo_data.R"))
#s1 = c("\nSuccessfully sourced logo_data.R")
#source(paste0(plot_script_path, "logo_data_msa.R"))
#s1 = c("\nSuccessfully sourced logo_data_msa.R")
#cat(s1)
# input data is merged_df3
# so repurposed it into a function so params can be passed instead to generate
# data required for plotting.
# Moved "logo_data.R" to redundant/
source(paste0(plot_script_path, "logo_data_msa.R"))
s1 = c("\nSuccessfully sourced logo_data_msa.R")
cat(s1)
####################################################################
# Data for DM OM Plots: WF and LF dfs
# My function: dm_om_wf_lf_data()
####################################################################
# My function: dm_om_wf_lf_data()
# location: scripts/functions/dm_om_data.R
#source("other_plots_data.R")
# converted to a function
# moved old one to redundant.
source(paste0(plot_script_path, "dm_om_data.R"))
s2 = c("\nSuccessfully sourced other_plots_data.R")
cat(s2)
####################################################################
#source(paste0(plot_script_path, "dm_om_data.R"))
#s2 = c("\nSuccessfully sourced other_plots_data.R")
#cat(s2)
####################################################################
# Data for Lineage barplots: WF and LF dfs
# My function: lineage_plot_data()
# location: scripts/functions/lineage_plot_data.R
####################################################################
source(paste0(plot_script_path, "lineage_data.R"))
#source(paste0(plot_script_path, "lineage_data.R"))
# converted to a function. Moved lineage_data.R to redundant/
lineage_dfL = lineage_plot_data(df = merged_df2
, lineage_column_name = "lineage"
, remove_empty_lineage = F
, lineage_label_col_name = "lineage_labels"
, id_colname = "id"
, snp_colname = "mutationinformation"
)
lin_wf = lineage_dfL[['lin_wf']]
lin_lf = lineage_dfL[['lin_lf']]
s3 = c("\nSuccessfully sourced lineage_data.R")
cat(s3)
@ -145,6 +142,7 @@ cat(s3)
####################################################################
# Data for corr plots:
# My function: corr_data_extract()
# location: scripts/functions/corr_plot_data.R
####################################################################
# make sure the above script works because merged_df2_combined is needed