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R code for slides extracted with knitr purl function 05_slides-stats.R
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## ----setup, include=FALSE--------------------------------------------------------
options(htmltools.dir.version = FALSE)
knitr::opts_chunk$set(
fig.width=9, fig.height=3.5, fig.retina=3,
out.width = "100%",
cache = FALSE,
echo = TRUE,
message = FALSE,
warning = FALSE,
hiline = TRUE,
comment = NA
)
options(width = 70)
#Load data...
#load(file = "Z:/Projects/Fridley_Brooke/2813_R_Programming_Course_2020/data/alldata.RData")
load(file = "Z:/Projects/Fridley_Brooke/2813_R_Programming_Course_2020/data/Rclassdata.RData")
library(easystats)
library(tidyverse)
library(kableExtra)
library(ggplot2)
library(janitor)
library(gridExtra)
library(broom)
Rclassdata %>% filter(acronym %in% c("KIRC","HNSC")) -> tcga
## ----xaringan-extras, echo=FALSE, results="asis"---------------------------------
# remotes::install_github("gadenbuie/xaringanExtra")
xaringanExtra::use_xaringan_extra(c(
"tile_view"
# "editable",
# "animate",
# "panelset"
))
## ----xaringan-panelset, echo=FALSE-----------------------------------------------
xaringanExtra::use_panelset()
## /* Define title slide image or logo here */
## .talk-logo {
## width: 400px;
## height: 750px;
## position: absolute;
## top: 6%;
## right: 7%;
## /* background-image: url('img/r4ds-cover.png'); */
## background-size: contain;
## background-repeat: no-repeat;
## background-position: contain;
## }
## ----comment=NA------------------------------------------------------------------
janitor::tabyl(tcga, radiation_therapy, vital_status )
## ----comment=NA------------------------------------------------------------------
janitor::tabyl(tcga, radiation_therapy, vital_status,
show_na = FALSE )
## ----comment=NA------------------------------------------------------------------
tcga %>%
tabyl(smoking, gender, show_na = FALSE )
## ----comment=NA------------------------------------------------------------------
tcga %>%
tabyl(smoking, gender, show_na = FALSE ) %>%
adorn_totals(where = c("row","col"))
## ----comment=NA------------------------------------------------------------------
tcga %>%
tabyl(smoking, gender, show_na = FALSE ) %>%
adorn_totals(where = c("row","col")) %>%
adorn_percentages(denominator = "col")
## ----comment=NA------------------------------------------------------------------
tcga %>%
tabyl(smoking, gender, show_na = FALSE ) %>%
adorn_totals(where = c("row","col")) %>%
adorn_percentages(denominator = "col") %>%
adorn_pct_formatting(digits = 0)
## ----comment=NA------------------------------------------------------------------
tcga %>%
tabyl(smoking, gender, show_na = FALSE ) %>%
adorn_totals(where = c("row","col")) %>%
adorn_percentages(denominator = "col") %>%
adorn_pct_formatting(digits = 0) %>%
adorn_ns(position = "front")
## ----chisqtest, echo=FALSE , include=TRUE---------------------------------------
tcga %>%
tabyl(smoking, gender, show_na = FALSE ) %>%
adorn_totals(where = c("row","col")) %>%
adorn_percentages(denominator = "col") %>%
adorn_pct_formatting(digits = 0) %>%
adorn_ns(position = "front")
## ----chisqtest1, eval=TRUE, include=TRUE----------------------------------------
tcga %>% tabyl( smoking, gender , show_na = FALSE ) %>%
chisq.test()
## ----geombar, echo = TRUE, fig.show = "hide"-------------------------------------
ggplot(tcga %>% filter(!is.na(smoking)),
aes(x = gender, fill = smoking )) +
geom_bar(position = "fill") +
labs(y = "proportion")
## ----ref.label = "geombar", echo = FALSE-----------------------------------------
## ----comment=NA------------------------------------------------------------------
tcga %>%
tabyl( gender, vital_status , show_na = FALSE ) %>%
adorn_totals(where = c("row","col")) %>%
adorn_percentages(denominator = "col") %>%
adorn_pct_formatting(digits = 0) %>%
adorn_ns(position = "front")
## ----comment=NA------------------------------------------------------------------
tcga %>% tabyl( gender, vital_status , show_na = FALSE ) %>%
fisher.test()
## ----geombar2, echo = TRUE-------------------------------------------------------
ggplot(tcga %>% filter(!is.na(vital_status)),
aes(x = gender, fill = vital_status )) +
geom_bar(position = "fill") + labs(y = "proportion")
## ----comment=NA------------------------------------------------------------------
r1 <- tcga %>% correlation::cor_test("DUOXA1_exp",
"DUOX1_exp",
method = c("pearson") )
r2 <- tcga %>% correlation::cor_test("BUB1_exp",
"C10orf32_exp",
method = c("pearson") )
r3 <- tcga %>% correlation::cor_test("BRAF_exp",
"DTL_exp",
method = c("pearson") )
## ----comment=NA------------------------------------------------------------------
knitr::kable(bind_rows(r1,r2,r3 ), format = 'html', digits = 3) %>%
kable_styling(font_size = 12)
## ----geom, echo = TRUE, fig.show = "hide"----------------------------------------
ggplot(tcga) +
aes(DUOXA1_exp, DUOX1_exp) +
geom_point() +
annotate(geom = "text", x = 10, y = 25000,
label = paste("r = ", round(r1$r, 2), sep = ""),
color = "red")
## ----ref.label = "geom", echo = FALSE--------------------------------------------
## ----geom2, echo = TRUE, fig.show = "hide"---------------------------------------
ggplot(tcga) +
aes(BUB1_exp, C10orf32_exp) +
geom_point() +
annotate(geom = "text", x = 1000, y = 4000,
label = paste("r = ", round(r2$r, 2), sep = ""),
color = "red")
## ----ref.label = "geom2", echo = FALSE-------------------------------------------
## ----geom3, echo = TRUE, fig.show = "hide"---------------------------------------
ggplot(tcga) +
aes(BRAF_exp, DTL_exp) +
geom_point() +
annotate(geom = "text", x = 0, y = 1100,
label = paste("r = ", round(r3$r, 2), sep = ""),
color = "red")
## ----ref.label = "geom3", echo = FALSE-------------------------------------------
## ----comment=NA------------------------------------------------------------------
## ----comment=NA------------------------------------------------------------------
tcga %>%
select(DUOXA1_exp, DUOX1_exp, BUB1_exp, BRAF_exp, DTL_exp ) %>%
cor() %>% round(.,2)
## ----echo=FALSE, comment=NA------------------------------------------------------
x <- seq(10,20,.25)
y <- (x-15)^3 + 100
pdata <- data.frame(x,y)
ggplot(pdata, aes(x,y)) + geom_point()
## ----comment=NA------------------------------------------------------------------
r1 <- tcga %>% correlation::cor_test("DUOXA1_exp",
"DUOX1_exp",
method = c("spearman") )
r2 <- tcga %>% correlation::cor_test("BUB1_exp",
"C10orf32_exp",
method = c("spearman") )
r3 <- tcga %>% correlation::cor_test("BRAF_exp",
"DTL_exp",
method = c("spearman") )
## ----comment=NA------------------------------------------------------------------
knitr::kable(bind_rows(r1, r2, r3), format = 'html', digits = 3) %>%
kable_styling(font_size = 12)
## ----ref.label = "wilcoxonhists", echo = FALSE-----------------------------------
## ----wilcoxonhists, echo = TRUE, fig.show = "hide"-------------------------------
mplot <- ggplot(tcga %>% filter(gender == "MALE"),
aes(x = BUB1_exp )) +
geom_histogram( colour = "black", position = "dodge") +
ggtitle("Males")
wplot <- ggplot(tcga %>% filter(gender == "FEMALE"),
aes(x = BUB1_exp)) +
geom_histogram( colour= "black", position = "dodge") +
ggtitle("Females")
grid.arrange(mplot,wplot, ncol=2)
## ----wilcoxonboxplots, echo = TRUE, fig.show = "hide"----------------------------
ggplot(tcga , aes(gender, BUB1_exp, fill = gender)) +
geom_boxplot() +
scale_fill_manual( values = c("yellow", "blue")) +
theme(legend.position = "none") +
labs(title = "BUB1 expression" , x = "Gender", y = "expression")
## ----ref.label = "wilcoxonboxplots", echo = FALSE--------------------------------
## ----comment=NA------------------------------------------------------------------
wilcox.test(BUB1_exp ~ gender, data = tcga,
alternative = c("two.sided"))
## ----t2boxplots, echo = TRUE, fig.show = "hide"----------------------------------
ggplot(tcga , aes(gender, PTEN_exp, fill = gender)) +
geom_boxplot() +
scale_fill_manual( values = c("yellow", "blue")) +
theme(legend.position = "none") +
labs(title = "PTEN expression" , x = "Gender", y = "expression")
## ----ref.label = "t2boxplots", echo = FALSE--------------------------------------
## ----comment=NA------------------------------------------------------------------
print(dim(tcga))
tcga <- tcga %>% filter(PTEN_exp < 4000)
print(dim(tcga))
## ----t2hist, echo = TRUE, fig.show = "hide"--------------------------------------
ggplot(tcga, aes(x=PTEN_exp, fill=gender)) +
scale_fill_manual( values = c("red", "blue")) +
geom_histogram( alpha=0.6, position="identity")
## ----ref.label = "t2hist", echo = FALSE------------------------------------------
## ----comment=NA------------------------------------------------------------------
t.test( tcga$PTEN_exp ~ tcga$gender,
alternative = c("two.sided"))
## ----echo=FALSE, comment=NA------------------------------------------------------
ggplot(tcga) +
aes(DUOXA1_exp, DUOX1_exp ) +
geom_point() +
annotate(geom = "text", x = 10, y = 25000,
label = paste("r = ", round(r1$r,2), sep = ""),
color = "red")
## ----echo=FALSE, comment=NA------------------------------------------------------
mod <- lm(DUOX1_exp ~ DUOXA1_exp, data = tcga)
print(summary(mod))
## ----comment=NA------------------------------------------------------------------
mod <- lm(DUOX1_exp ~ DUOXA1_exp, data = tcga)
tidy(mod)
## ----comment=NA------------------------------------------------------------------
knitr::kable(tidy(mod), format = 'html', digits = 3) %>%
kable_styling(font_size = 22)
## ----echo=FALSE, comment=NA------------------------------------------------------
ggplot(tcga, aes(DUOXA1_exp, DUOX1_exp )) +
geom_point() +
annotate(geom = "text", x = 10, y = 25000,
label = paste("r = ", round(r1$r,2), sep = ""),
color = "red") +
geom_smooth(method = 'lm')
## ----echo=FALSE, comment=NA------------------------------------------------------
knitr::kable(tidy(mod), format = 'html', digits = 3) %>% kable_styling(font_size = 22)