plotGraph: Plot scatter graph of proportion against DDD per 1000

In blue-moon22/resistomeAnalysis: Resistome Analysis

Description

Plot scatter graph of proportion against DDD per 1000

Usage

plotGraph(data_merge, Location, class_cols, shape_values)

Arguments

data_merge	A dataframe of proportions containing ARG classes and confidence intervals, and resistanceMap DDD per 1000
Location	A string of a Location e.g. "US"
class_cols	A character vector of colours, named by ARG class

Value

None

Examples

library(RColorBrewer)
df_map <- readMappingData("/home/vicky/Documents/CHMI/Resistome-paper/resistomeAnalysis/db/MAPPING_DATA/nonsubsampled_merged.csv", without_US_duplicates = TRUE)
df_map_pb_saliva_class <- joinProportionAndBootstrap(df_map, "Drug.Class", "saliva")
df_map_pb_dental_class <- joinProportionAndBootstrap(df_map, "Drug.Class", "dental")
rm_use_card <- readResistanceMapUseData("/home/vicky/Documents/CHMI/Resistome-paper/resistomeAnalysis/db/ResistanceMap/resistanceMap_use.csv")
data_merge <- mergeData(list(saliva = df_map_pb_saliva_class, dental = df_map_pb_dental_class), rm_use_card)

cols <- brewer.pal(length(unique(data_merge$class)), "Paired")
names(cols) <- unique(data_merge$class)
plotGraph(data_merge, "US", cols)

blue-moon22/resistomeAnalysis documentation built on Jan. 17, 2020, 4:15 a.m.