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SNP -> SAV for thesis plots

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This commit is contained in:
Tanushree Tunstall 2023-02-19 17:43:22 +00:00
parent 777d3765cf
commit db7e2912e1
31 changed files with 145 additions and 145 deletions
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2
scripts/functions/tests/test_bp.R
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@ -62,7 +62,7 @@ lig_dist = 10
stability_count_bp(plotdf = my_df_u_lig
, df_colname = "ligand_outcome"
, leg_title = "Ligand outcome"
, yaxis_title = paste0("Number of nsSNPs\nLigand dist: <", lig_dist, "\u212b")
, yaxis_title = paste0("Number of SAVs\nLigand dist: <", lig_dist, "\u212b")
#, bp_plot_title = "Sites < 10 Ang of ligand"
)

6
scripts/functions/tests/test_bp_lineage.R
View file

@ -4,7 +4,7 @@ source ('get_plotting_dfs.R')
source("../functions/bp_lineage.R")
#########################################
# Lineage and SNP count: lineage lf data
# Lineage and SAV count: lineage lf data
#########################################
#=========================
# Data: All lineages or
@ -35,7 +35,7 @@ lin_count_bp(lin_lf_plot = lin_lf
, y_label = "Count")
###############################################
# Lineage SNP diversity count: lineage wf data
# Lineage SAV diversity count: lineage wf data
###############################################
#=========================
# Data: All lineages or
@ -59,4 +59,4 @@ lin_count_bp(lin_wf_plot = lin_wf
, x_lab_angle = 90
, my_xats = 20
, y_scale_percent = T
, y_label = "SNP diversity")
, y_label = "SAV diversity")

6
scripts/functions/tests/test_logo_plots.R
View file

@ -37,7 +37,7 @@ LP1<- LogoPlotCustomH (plot_df = merged_df3
)
########################################
# Logo plot showing nsSNPs by positions
# Logo plot showing SAVs by positions
# wild-type and mutant aa
# script: logoP_snp.R
########################################
@ -48,7 +48,7 @@ LP2<- LogoPlotSnps(plot_df = merged_df3
, omit_snp_count = c(0)# can be 0,1, 2, etc.# DD
, my_logo_col = "chemistry" #DD
, x_lab = "Wild-type position"
, y_lab = "nsSNP count"
, y_lab = "SAV count"
, x_ats = 10
, x_tangle = 90
, y_ats = 15
@ -87,7 +87,7 @@ LP3<- LogoPlotMSA(unified_msa
, x_axis_offset_filtered = 0.05
, y_axis_offset = 0.05
#, y_breaks = c(0, 2, 4, 6, 8, 10, 12)
, x_lab_mut = "nsSNP-position"
, x_lab_mut = "SAV-position"
#, y_lab_mut
, x_ats = 10
, x_tangle = 90