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<!DOCTYPE html>
<html lang="" xml:lang="">
<head>
<title>Swimmer Plots in R using ggplot</title>
<meta charset="utf-8" />
<meta name="author" content="Kat Hoffman" />
<script src="libs/header-attrs-2.13/header-attrs.js"></script>
<link href="libs/pagedtable-1.1/css/pagedtable.css" rel="stylesheet" />
<script src="libs/pagedtable-1.1/js/pagedtable.js"></script>
<link rel="stylesheet" href="xaringan-themer.css" type="text/css" />
<link rel="stylesheet" href="extra.css" type="text/css" />
</head>
<body>
<textarea id="source">
layout: true
<div class="my-footer"><span>kathoffman.github.io/swimmer-plots/slides-wcm.html</span></div>
---
name: xaringan-title
class: right, middle
background-image: url(img/blue-foaming-waves-north-beach-nazare-portugal.jpg)
background-size: cover
<h1 style="color: white;">Making swimmer plots for longitudinal data using {ggplot}</h1>
<img src="img/rmed-hex.png" alt="Rmed-hex-sticker" width="180" />
<h3 style="color: white;">Kat Hoffman | WCM Computing Club | September 6, 2022</h3>
---
# Swimmer plot
.pull-left[
- Graphical way to show a **subject's profile over time**
- A series of horizontal lines, in which **each line represents one subject**
- **Colors or shapes** on the line **indicate treatments** or other statuses of that subject at a particular time
]
.pull-right[
<div class="figure" style="text-align: center">
<img src="img/cell_swimmer.png" alt="Image: Shen et al. Cell 182, 59–72, July 9, 2020" width="600" />
<p class="caption">Image: Shen et al. Cell 182, 59–72, July 9, 2020</p>
</div>
]
<!-- -- -->
<!-- - -->
<!-- -- -->
<!-- - -->
<!-- -- -->
<!-- - Excellent for exploratory data analysis (EDA) of longitudinal data (e.g. visualize missigness or sampling patterns) -->
<!-- -- -->
<!-- - Can be included as a final product (e.g. manuscripts, presentations) to explain cohort composition, treatment variability, and more -->
<!-- -- -->
<!-- - While `R` packages such as `swimmer` exist, it is often faster and more customizable to write end-to-end `ggplot` code yourself -->
---
# Do we *really* have to hand-code this?
.pull-left[
- `R` packages such as `swimplot` do exist, but it is more customizable to write end-to-end `ggplot` code yourself
- Configuring the legend correctly in `ggplot` can be tricky whether you use `swimplot` or not
]
.pull-right[
<div class="figure">
<img src="img/swimmer_swimplot.png" alt="Image courtesy of {swimplot} vignette." width="500" />
<p class="caption">Image courtesy of {swimplot} vignette.</p>
</div>
]
---
.left-column[
### Today's swimmer plot:
We will show the timing of...
- severe hypoxia
- intubation
- steroids administration
- 28-day mortality
...in a cohort of hospitalized COVID-19 patients.
]
.right-column[
<img src="img/swimmer.png" width="700" style="display: block; margin: auto;" />
]
---
# Step 1: Long-form data set
.pull-left[
- ID column
- Time column (e.g. day)
- One column per status (e.g. drug A - yes/no, drug B - yes/no)
- One row per subject per unit of time
]
--
.pull-right[
```r
library(tidyverse)
library(data.table)
dat_long <- read_csv("https://raw.githubusercontent.com/kathoffman/steroids-trial-emulation/main/data/dat_trt_timeline.csv",col_types = list(id = "c", steroids = "c", death = "c", severe = "c"))
dat_long |> data.table()
```
```
id day intubation_status steroids death severe
1: 797 0 Not intubated 0 0 0
2: 797 1 Not intubated 0 0 0
3: 797 2 Not intubated 0 0 1
4: 797 3 Not intubated 0 0 0
5: 797 4 Not intubated 0 0 0
---
415: 664 27 Not intubated 0 0 0
416: 664 28 Not intubated 0 0 0
417: 373 0 Not intubated 0 0 0
418: 373 1 Not intubated 0 0 0
419: 373 2 Not intubated 0 0 0
```
]
---
# Step 2: Long-form data for plotting
.pull-left[
- ID column (**optional: order by maximum time per subject**)
- Time column
- One column per status, **which is now the time if you want the status to be marked on the plot**
- One row per subject per unit of time
]
--
.pull-right[
This is a way to create data with a reordered patient ID (by hospital length-of-stay):
```r
dat_reorder <-
dat_long |>
group_by(id) |>
mutate(max_day = max(day)) |>
ungroup() |>
mutate(id = fct_reorder(factor(id), max_day))
```
The next slide shows how to change the status columns to `{status}_this_day` columns.
]
---
# Step 2: Long-form data for plotting
```r
dat_swim <- dat_reorder |>
mutate(severe_this_day = case_when(severe == 1 ~ day),
steroids_this_day = case_when(steroids == 1 ~ day),
death_this_day = case_when(death == 1 ~ day))
dat_swim |> paged_table()
```
<div data-pagedtable="false">
<script data-pagedtable-source type="application/json">
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intubated","4":"0","5":"0","6":"0","7":"16","8":"NA","9":"NA","10":"NA"},{"1":"705","2":"13","3":"Not intubated","4":"0","5":"0","6":"0","7":"16","8":"NA","9":"NA","10":"NA"},{"1":"705","2":"14","3":"Not intubated","4":"0","5":"0","6":"0","7":"16","8":"NA","9":"NA","10":"NA"},{"1":"705","2":"15","3":"Not intubated","4":"0","5":"0","6":"0","7":"16","8":"NA","9":"NA","10":"NA"},{"1":"705","2":"16","3":"Not intubated","4":"0","5":"1","6":"0","7":"16","8":"NA","9":"NA","10":"16"},{"1":"784","2":"0","3":"Not intubated","4":"0","5":"0","6":"0","7":"4","8":"NA","9":"NA","10":"NA"},{"1":"784","2":"1","3":"Not intubated","4":"0","5":"0","6":"0","7":"4","8":"NA","9":"NA","10":"NA"},{"1":"784","2":"2","3":"Not intubated","4":"0","5":"0","6":"0","7":"4","8":"NA","9":"NA","10":"NA"},{"1":"784","2":"3","3":"Not intubated","4":"0","5":"0","6":"0","7":"4","8":"NA","9":"NA","10":"NA"},{"1":"784","2":"4","3":"Not intubated","4":"0","5":"0","6":"0","7":"4","8":"NA","9":"NA","10":"NA"},{"1":"664","2":"0","3":"Not intubated","4":"0","5":"0","6":"0","7":"28","8":"NA","9":"NA","10":"NA"},{"1":"664","2":"1","3":"Not intubated","4":"0","5":"0","6":"0","7":"28","8":"NA","9":"NA","10":"NA"},{"1":"664","2":"2","3":"Not intubated","4":"0","5":"0","6":"1","7":"28","8":"2","9":"NA","10":"NA"},{"1":"664","2":"3","3":"Not intubated","4":"0","5":"0","6":"0","7":"28","8":"NA","9":"NA","10":"NA"},{"1":"664","2":"4","3":"Not intubated","4":"0","5":"0","6":"0","7":"28","8":"NA","9":"NA","10":"NA"},{"1":"664","2":"5","3":"Not intubated","4":"0","5":"0","6":"0","7":"28","8":"NA","9":"NA","10":"NA"},{"1":"664","2":"6","3":"Not intubated","4":"0","5":"0","6":"0","7":"28","8":"NA","9":"NA","10":"NA"},{"1":"664","2":"7","3":"Not intubated","4":"0","5":"0","6":"0","7":"28","8":"NA","9":"NA","10":"NA"},{"1":"664","2":"8","3":"Not intubated","4":"0","5":"0","6":"0","7":"28","8":"NA","9":"NA","10":"NA"},{"1":"664","2":"9","3":"Not intubated","4":"0","5":"0","6":"0","7":"28","8":"NA","9":"NA","10":"NA"},{"1":"664","2":"10","3":"Not intubated","4":"0","5":"0","6":"0","7":"28","8":"NA","9":"NA","10":"NA"},{"1":"664","2":"11","3":"Not intubated","4":"0","5":"0","6":"0","7":"28","8":"NA","9":"NA","10":"NA"},{"1":"664","2":"12","3":"Not intubated","4":"0","5":"0","6":"0","7":"28","8":"NA","9":"NA","10":"NA"},{"1":"664","2":"13","3":"Not intubated","4":"0","5":"0","6":"0","7":"28","8":"NA","9":"NA","10":"NA"},{"1":"664","2":"14","3":"Not intubated","4":"0","5":"0","6":"0","7":"28","8":"NA","9":"NA","10":"NA"},{"1":"664","2":"15","3":"Not intubated","4":"0","5":"0","6":"0","7":"28","8":"NA","9":"NA","10":"NA"},{"1":"664","2":"16","3":"Not intubated","4":"0","5":"0","6":"0","7":"28","8":"NA","9":"NA","10":"NA"},{"1":"664","2":"17","3":"Not intubated","4":"0","5":"0","6":"0","7":"28","8":"NA","9":"NA","10":"NA"},{"1":"664","2":"18","3":"Not intubated","4":"0","5":"0","6":"0","7":"28","8":"NA","9":"NA","10":"NA"},{"1":"664","2":"19","3":"Not intubated","4":"0","5":"0","6":"0","7":"28","8":"NA","9":"NA","10":"NA"},{"1":"664","2":"20","3":"Not intubated","4":"0","5":"0","6":"0","7":"28","8":"NA","9":"NA","10":"NA"},{"1":"664","2":"21","3":"Not intubated","4":"0","5":"0","6":"0","7":"28","8":"NA","9":"NA","10":"NA"},{"1":"664","2":"22","3":"Not intubated","4":"0","5":"0","6":"0","7":"28","8":"NA","9":"NA","10":"NA"},{"1":"664","2":"23","3":"Not intubated","4":"0","5":"0","6":"0","7":"28","8":"NA","9":"NA","10":"NA"},{"1":"664","2":"24","3":"Not intubated","4":"0","5":"0","6":"0","7":"28","8":"NA","9":"NA","10":"NA"},{"1":"664","2":"25","3":"Not intubated","4":"0","5":"0","6":"0","7":"28","8":"NA","9":"NA","10":"NA"},{"1":"664","2":"26","3":"Not intubated","4":"0","5":"0","6":"0","7":"28","8":"NA","9":"NA","10":"NA"},{"1":"664","2":"27","3":"Not intubated","4":"0","5":"0","6":"0","7":"28","8":"NA","9":"NA","10":"NA"},{"1":"664","2":"28","3":"Not intubated","4":"0","5":"0","6":"0","7":"28","8":"NA","9":"NA","10":"NA"},{"1":"373","2":"0","3":"Not intubated","4":"0","5":"0","6":"0","7":"2","8":"NA","9":"NA","10":"NA"},{"1":"373","2":"1","3":"Not intubated","4":"0","5":"0","6":"0","7":"2","8":"NA","9":"NA","10":"NA"},{"1":"373","2":"2","3":"Not intubated","4":"0","5":"0","6":"0","7":"2","8":"NA","9":"NA","10":"NA"}],"options":{"columns":{"min":{},"max":[10]},"rows":{"min":[10],"max":[10]},"pages":{}}}
</script>
</div>
---
count: false
# Step 3: Plot all your geometries
.panel1-swim0-user[
```r
*dat_swim %>%
* ggplot(aes(y=id, group=id))
```
]
.panel2-swim0-user[
<!-- -->
]
---
count: false
# Step 3: Plot all your geometries
.panel1-swim0-user[
```r
dat_swim %>%
ggplot(aes(y=id, group=id)) +
* theme_bw()
```
]
.panel2-swim0-user[
<!-- -->
]
---
count: false
# Step 3: Plot all your geometries
.panel1-swim0-user[
```r
dat_swim %>%
ggplot(aes(y=id, group=id)) +
theme_bw() +
* geom_line(aes(x=day, col = intubation_status))
```
]
.panel2-swim0-user[
<!-- -->
]
---
count: false
# Step 3: Plot all your geometries
.panel1-swim0-user[
```r
dat_swim %>%
ggplot(aes(y=id, group=id)) +
theme_bw() +
geom_line(aes(x=day, col = intubation_status)) +
* geom_point(aes(x=steroids_this_day))
```
]
.panel2-swim0-user[
<!-- -->
]
---
count: false
# Step 3: Plot all your geometries
.panel1-swim0-user[
```r
dat_swim %>%
ggplot(aes(y=id, group=id)) +
theme_bw() +
geom_line(aes(x=day, col = intubation_status)) +
geom_point(aes(x=steroids_this_day)) +
* geom_point(aes(x=severe_this_day))
```
]
.panel2-swim0-user[
<!-- -->
]
---
count: false
# Step 3: Plot all your geometries
.panel1-swim0-user[
```r
dat_swim %>%
ggplot(aes(y=id, group=id)) +
theme_bw() +
geom_line(aes(x=day, col = intubation_status)) +
geom_point(aes(x=steroids_this_day)) +
geom_point(aes(x=severe_this_day)) +
* geom_point(aes(x=death_this_day))
```
]
.panel2-swim0-user[
<!-- -->
]
<style>
.panel1-swim0-user {
color: black;
width: 38.6060606060606%;
hight: 32%;
float: left;
padding-left: 1%;
font-size: 80%
}
.panel2-swim0-user {
color: black;
width: 59.3939393939394%;
hight: 32%;
float: left;
padding-left: 1%;
font-size: 80%
}
.panel3-swim0-user {
color: black;
width: NA%;
hight: 33%;
float: left;
padding-left: 1%;
font-size: 80%
}
</style>
---
count: false
# Step 4: Modify geom_* layers.
.panel1-swim1-user[
```r
*dat_swim %>%
* ggplot(aes(y=id, group=id)) +
* theme_bw()
```
]
.panel2-swim1-user[
<!-- -->
]
---
count: false
# Step 4: Modify geom_* layers.
.panel1-swim1-user[
```r
dat_swim %>%
ggplot(aes(y=id, group=id)) +
theme_bw() +
* geom_line(aes(x=day, col = intubation_status),
* size=1.8)
```
]
.panel2-swim1-user[
<!-- -->
]
---
count: false
# Step 4: Modify geom_* layers.
.panel1-swim1-user[
```r
dat_swim %>%
ggplot(aes(y=id, group=id)) +
theme_bw() +
geom_line(aes(x=day, col = intubation_status),
size=1.8) +
* geom_point(aes(x=steroids_this_day),
* stroke=2,
* shape = 15)
```
]
.panel2-swim1-user[
<!-- -->
]
---
count: false
# Step 4: Modify geom_* layers.
.panel1-swim1-user[
```r
dat_swim %>%
ggplot(aes(y=id, group=id)) +
theme_bw() +
geom_line(aes(x=day, col = intubation_status),
size=1.8) +
geom_point(aes(x=steroids_this_day),
stroke=2,
shape = 15) +
* geom_point(aes(x=severe_this_day),
* size=2,
* stroke=1.5,
* shape = 21)
```
]
.panel2-swim1-user[
<!-- -->
]
---
count: false
# Step 4: Modify geom_* layers.
.panel1-swim1-user[
```r
dat_swim %>%
ggplot(aes(y=id, group=id)) +
theme_bw() +
geom_line(aes(x=day, col = intubation_status),
size=1.8) +
geom_point(aes(x=steroids_this_day),
stroke=2,
shape = 15) +
geom_point(aes(x=severe_this_day),
size=2,
stroke=1.5,
shape = 21) +
* geom_point(aes(x=death_this_day),
* size=2,
* stroke=1.5,
* shape = 4)
```
]
.panel2-swim1-user[
<!-- -->
]
<style>
.panel1-swim1-user {
color: black;
width: 38.6060606060606%;
hight: 32%;
float: left;
padding-left: 1%;
font-size: 80%
}
.panel2-swim1-user {
color: black;
width: 59.3939393939394%;
hight: 32%;
float: left;
padding-left: 1%;
font-size: 80%
}
.panel3-swim1-user {
color: black;
width: NA%;
hight: 33%;
float: left;
padding-left: 1%;
font-size: 80%
}
</style>
---
# Step 5: Add colors and legend
.left-column[
]
.right-column[
**The Big Picture:**
- We want a legend which correctly maps each shape, color, and line type to the corresponding status.
- We need all of our statuses to show up in the legend. They currently do not, because they're not being mapped to an `aes`thetic argument.
- We will force all the statuses to show up by creating a new aesthetic (color) which **corresponds to the name we want each status to be labeled** in the legend.
- We will then modify this legend for "color" to also contain information about shape, linetype, etc. for each status.
]
---
count: false
# Step 5: Add colors and legend
.panel1-swim2-user[
```r
*dat_swim %>%
* ggplot(aes(y=id)) +
* theme_bw() +
* geom_line(aes(x=day,
* col = intubation_status,
* group=id),
* size=1.8)
```
]
.panel2-swim2-user[
<!-- -->
]
---
count: false
# Step 5: Add colors and legend
.panel1-swim2-user[
```r
dat_swim %>%
ggplot(aes(y=id)) +
theme_bw() +
geom_line(aes(x=day,
col = intubation_status,
group=id),
size=1.8) +
* geom_point(aes(x=steroids_this_day,
* col="Steroids"),
* stroke=2,
* shape=15)
```
]
.panel2-swim2-user[
<!-- -->
]
---
count: false
# Step 5: Add colors and legend
.panel1-swim2-user[
```r
dat_swim %>%
ggplot(aes(y=id)) +
theme_bw() +
geom_line(aes(x=day,
col = intubation_status,
group=id),
size=1.8) +
geom_point(aes(x=steroids_this_day,
col="Steroids"),
stroke=2,
shape=15) +
* geom_point(aes(x=severe_this_day,
* col="Severe hypoxia"),
* size=2,
* stroke=1.5,
* shape=21)
```
]
.panel2-swim2-user[
<!-- -->
]
---
count: false
# Step 5: Add colors and legend
.panel1-swim2-user[
```r
dat_swim %>%
ggplot(aes(y=id)) +
theme_bw() +
geom_line(aes(x=day,
col = intubation_status,
group=id),
size=1.8) +
geom_point(aes(x=steroids_this_day,
col="Steroids"),
stroke=2,
shape=15) +
geom_point(aes(x=severe_this_day,
col="Severe hypoxia"),
size=2,
stroke=1.5,
shape=21) +
* geom_point(aes(x=death_this_day,
* col="Death"),
* size=2,
* stroke=1.5,
* shape=4)
```
]
.panel2-swim2-user[
<!-- -->
]
<style>
.panel1-swim2-user {
color: black;
width: 38.6060606060606%;
hight: 32%;
float: left;
padding-left: 1%;
font-size: 80%
}
.panel2-swim2-user {
color: black;
width: 59.3939393939394%;
hight: 32%;
float: left;
padding-left: 1%;
font-size: 80%
}
.panel3-swim2-user {
color: black;
width: NA%;
hight: 33%;
float: left;
padding-left: 1%;
font-size: 80%
}
</style>
---
# Step 6: Modify colors
- We now need a key for status labels and corresponding colors.
```r
# define colors for all geometries with a color argument
cols <- c("Severe hypoxia" = "#b24745", # red
"Intubated" = "#483d8b", # navy
"Not intubated" = "#74aaff", # blue
"Steroids"="#ffd966", # gold
"Death" = "#000000") # black
```
- The label of the status should match the label inputted to `aes(col = "...")`.
- The order of this color key will be the order the statuses appear in the legend.
- We will use this key as the `values` argument of `scale_color_manual()`:
---
count: false
# Step 6: Modify colors
.panel1-swim3-user[
```r
*dat_swim %>%
* ggplot(aes(y=id)) +
* theme_bw() +
* geom_line(aes(x=day,
* col = intubation_status,
* group=id),
* size=1.8) +
* geom_point(aes(x=steroids_this_day,
* col="Steroids"),
* stroke=2,
* shape=15) +
* geom_point(aes(x=severe_this_day,
* col="Severe hypoxia"),
* size=2,
* stroke=1.5,
* shape=21) +
* geom_point(aes(x=death_this_day,
* col="Death"),
* size=2,
* stroke=1.5,
* shape=4)
```
]
.panel2-swim3-user[
<!-- -->
]
---
count: false
# Step 6: Modify colors
.panel1-swim3-user[
```r
dat_swim %>%
ggplot(aes(y=id)) +
theme_bw() +
geom_line(aes(x=day,
col = intubation_status,
group=id),
size=1.8) +
geom_point(aes(x=steroids_this_day,
col="Steroids"),
stroke=2,
shape=15) +
geom_point(aes(x=severe_this_day,
col="Severe hypoxia"),
size=2,
stroke=1.5,
shape=21) +
geom_point(aes(x=death_this_day,
col="Death"),
size=2,
stroke=1.5,
shape=4) +
* scale_color_manual(values = cols,
* name="Patient Status")
```
]
.panel2-swim3-user[
<!-- -->
]
<style>
.panel1-swim3-user {
color: black;
width: 38.6060606060606%;
hight: 32%;
float: left;
padding-left: 1%;
font-size: 80%
}
.panel2-swim3-user {
color: black;
width: 59.3939393939394%;
hight: 32%;
float: left;
padding-left: 1%;
font-size: 80%
}
.panel3-swim3-user {
color: black;
width: NA%;
hight: 33%;
float: left;
padding-left: 1%;
font-size: 80%
}
</style>
---
# Step 7: Modify legend using override.aes()
- We need to create vectors for overriding the aesthetics for `shape`, `linetype`, `stroke`, and `size` in the current "color" legend.
- These should be in the same order as the `cols` key
- If we don't want a certain aesthetic to show up (e.g. no shape for intubation), we use `NA`
```r
cols
```
```
Severe hypoxia Intubated Not intubated Steroids Death
"#b24745" "#483d8b" "#74aaff" "#ffd966" "#000000"
```
```r
shape_override <- c(21, NA, NA, 15, 4) # order matches `cols`:severe, intubation (yes/no), steroids, death
line_override <- c(NA,1,1,NA,NA) # order matches `cols`:severe, intubation (yes/no), steroids, death
stroke_override <- c(.8,1,1,1,1) # order matches `cols`:severe, intubation (yes/no), steroids, death
size_override <- c(2.5,2.5,2.6,2,2) # order matches `cols`:severe, intubation (yes/no), steroids, death
```
---
count: false
# Step 7: Modify legend using override.aes()
.panel1-swim4-user[
```r
*dat_swim %>%
* ggplot(aes(y=id)) +
* theme_bw() +
* geom_line(aes(x=day, col = intubation_status, group=id),
* size=1.8) +
* geom_point(aes(x=steroids_this_day, col="Steroids"),
* stroke=2, shape=15) +
* geom_point(aes(x=severe_this_day, col="Severe hypoxia"),
* size=2, stroke=1.5, shape=21) +
* geom_point(aes(x=death_this_day, col="Death"),
* size=2, stroke=1.5, shape=4) +
* scale_color_manual(values = cols,
* name="Patient Status")
```
]
.panel2-swim4-user[
<!-- -->
]
---
count: false
# Step 7: Modify legend using override.aes()
.panel1-swim4-user[
```r
dat_swim %>%
ggplot(aes(y=id)) +
theme_bw() +
geom_line(aes(x=day, col = intubation_status, group=id),
size=1.8) +
geom_point(aes(x=steroids_this_day, col="Steroids"),
stroke=2, shape=15) +
geom_point(aes(x=severe_this_day, col="Severe hypoxia"),
size=2, stroke=1.5, shape=21) +
geom_point(aes(x=death_this_day, col="Death"),
size=2, stroke=1.5, shape=4) +
scale_color_manual(values = cols,
name="Patient Status") +
* guides(color = guide_legend(
* override.aes = list(
* stroke = stroke_override,
* size = size_override,
* shape = shape_override,
* linetype = line_override)
* ))
```
]
.panel2-swim4-user[
<!-- -->
]
<style>
.panel1-swim4-user {
color: black;
width: 38.6060606060606%;
hight: 32%;
float: left;
padding-left: 1%;
font-size: 80%
}
.panel2-swim4-user {
color: black;
width: 59.3939393939394%;
hight: 32%;
float: left;
padding-left: 1%;
font-size: 80%
}
.panel3-swim4-user {
color: black;
width: NA%;
hight: 33%;
float: left;
padding-left: 1%;
font-size: 80%
}
</style>
---
count: false
# Step 8: Make minor theme edits
.panel1-swim5-user[
```r
*p + labs(x="Days since hospitalization",
* y="Patient\nnumber",
* title="Treatment Timeline for N=30 Patients")
```
]
.panel2-swim5-user[
<!-- -->
]
---
count: false
# Step 8: Make minor theme edits
.panel1-swim5-user[
```r
p + labs(x="Days since hospitalization",
y="Patient\nnumber",
title="Treatment Timeline for N=30 Patients") +
* scale_x_continuous(expand=c(0,0))
```
]
.panel2-swim5-user[
<!-- -->
]
---
count: false
# Step 8: Make minor theme edits
.panel1-swim5-user[
```r
p + labs(x="Days since hospitalization",
y="Patient\nnumber",
title="Treatment Timeline for N=30 Patients") +
scale_x_continuous(expand=c(0,0)) +
* theme(text=element_text(family="Poppins", size=11)) +
* theme(title = element_text(angle = 0, vjust=.5,
* size=12, face="bold"),
* axis.title.y = element_text(angle = 0, vjust=.5,
* size=12, face="bold"),
* axis.title.x = element_text(size=15, face="bold",
* vjust=-0.5, hjust=0),
* axis.text.y = element_text(size=6,
* hjust=1.5),
* axis.ticks.y = element_blank())
```
]
.panel2-swim5-user[
<!-- -->
]
---
count: false
# Step 8: Make minor theme edits
.panel1-swim5-user[
```r
p + labs(x="Days since hospitalization",
y="Patient\nnumber",
title="Treatment Timeline for N=30 Patients") +
scale_x_continuous(expand=c(0,0)) +
theme(text=element_text(family="Poppins", size=11)) +
theme(title = element_text(angle = 0, vjust=.5,
size=12, face="bold"),
axis.title.y = element_text(angle = 0, vjust=.5,
size=12, face="bold"),
axis.title.x = element_text(size=15, face="bold",
vjust=-0.5, hjust=0),
axis.text.y = element_text(size=6,
hjust=1.5),
axis.ticks.y = element_blank()) +
* theme(legend.position = c(0.8, 0.3),
* legend.title = element_text(colour="black",
* size=13,
* face=4),
* legend.text = element_text(colour="black",
* size=10),