Nothing
## ----setup, include = FALSE---------------------------------------------------
knitr::opts_chunk$set(
collapse = TRUE,
comment = "#>",
fig.width = 6,
fig.height = 4
)
data.table::setDTthreads(1L)
## ----load_data----------------------------------------------------------------
library("hagis")
head(P_sojae_survey)
## ----remove-gene--------------------------------------------------------------
P_sojae_survey$Rps <-
gsub(pattern = "Rps ",
replacement = "",
x = P_sojae_survey$Rps)
head(P_sojae_survey)
## ----example-function, eval=FALSE---------------------------------------------
# Rps.summary <- summarize_gene(
# x = P_sojae_survey,
# cutoff = 60,
# control = "susceptible",
# sample = "Isolate",
# gene = "Rps",
# perc_susc = "perc.susc"
# )
## ----shared-args--------------------------------------------------------------
hagis_args <- list(
x = P_sojae_survey,
cutoff = 60,
control = "susceptible",
sample = "Isolate",
gene = "Rps",
perc_susc = "perc.susc"
)
## ----echo=TRUE----------------------------------------------------------------
Rps.summary <- do.call(summarize_gene, hagis_args)
Rps.summary
## ----pander-print-Rps, echo=TRUE----------------------------------------------
library(pander)
pander(Rps.summary)
## ----plot-summary, echo=TRUE--------------------------------------------------
autoplot(Rps.summary, type = "percentage")
autoplot(Rps.summary, type = "count")
## ----complexities, echo=TRUE, message=FALSE, warning=FALSE--------------------
complexities <- do.call(calculate_complexities, hagis_args)
complexities
## ----pander-print-complexities------------------------------------------------
pander(complexities$grouped_complexities)
pander(complexities$indvidual_complexities)
## ----summary-complexities-----------------------------------------------------
pander(summary(complexities))
## ----complexities-plot--------------------------------------------------------
autoplot(complexities, type = "percentage")
autoplot(complexities, type = "count")
## ----calculate-diversities, echo=TRUE-----------------------------------------
diversity <- do.call(calculate_diversities, hagis_args)
diversity
## ----diversity-pander---------------------------------------------------------
pander(diversity)
## ----diversities-table--------------------------------------------------------
diversities_table(diversity)
## ----individual-pathotypes----------------------------------------------------
individual_pathotypes(diversity)
## ----set-up-adv.plot----------------------------------------------------------
library(ggplot2)
Rps.plot <- autoplot(Rps.summary, type = "percentage")
Rps.plot
## ----change-plot-theme--------------------------------------------------------
Rps.plot <- Rps.plot +
theme_minimal()
Rps.plot
## ----change-plot-font---------------------------------------------------------
Rps.plot <- Rps.plot +
theme(text = element_text(face = "bold", family = "serif"))
Rps.plot
## ----horizontal-plot----------------------------------------------------------
Rps.plot <- Rps.plot +
coord_flip()
Rps.plot
## ----use-Colors---------------------------------------------------------------
autoplot(Rps.summary, type = "percentage", color = "#18453b") +
theme_bw() +
theme(text = element_text(face = "bold", family = "serif"))
## ----sort-axis----------------------------------------------------------------
autoplot(
Rps.summary,
type = "percentage",
color = "#18453b",
order = "ascending"
) +
theme_bw() +
theme(text = element_text(face = "bold", family = "serif"))
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