Cannot display graphs with knitr to pdf

Publishing Your Results
1

This is how I am using knitr to display a plot. I get the message "df_max cannot be found" so it seems that df_max is not globally used by the knitr code. Could you help with this?

# Initialize device
dev.new(width =20000, height = 10000, unit = "px")

# Plot the event types that cause the largest number of injuries across all the states in the USA. Include the summary statistics table on the graph
p1 <- ggplot(df_max, aes(EVTYPE, INJURIES)) + geom_point(color = "blue") + theme(legend.position="top") + 
 		  theme(axis.text.x = element_text(color = "grey20", size = 7.0, angle = 90, hjust = .5, vjust = .5, face = "plain"),     
   		  axis.text.y = element_text(color = "grey20", size = 5, angle = 50, hjust = 0.5, vjust = 0, face = "plain")) +
              ggtitle("Health Inpact - INJURIES - of Severe Storms Across the USA") +
		  theme(plot.title = element_text(size = 10, face = "bold")) +
		  xlab("STORM EVENT TYPE") +
		  theme(axis.title.y = element_text(size = rel(0.5), angle = 90), axis.title=element_text(size=14,face="bold")) +
    		  theme(axis.title.x = element_text(size = rel(0.5), angle = 0), axis.title=element_text(size=14,face="bold")) +
              annotation_custom(tableGrob(round(stats, digits = 3), theme=ttheme_minimal(base_size = 7)))


# Plot the events causing the maximum amount of property damage across cost1a states. Include the summary statistics table on the graph.
p2 <- ggplot(cost1a_max, aes(EVTYPE, PROPDMG)) + geom_point(color = "blue") + theme(legend.position="top") + 
 		  theme(axis.text.x = element_text(color = "grey20", size = 7.0, angle = 90, hjust = .5, vjust = .5, face = "plain"),     
  		  axis.text.y = element_text(color = "grey20", size = 5, angle = 50, hjust = 0.5, vjust = 0, face = "plain")) +
              ggtitle("Economic Inpact - PROPERTY DAMAGE - of Severe Storms across the states of GU, TX, AK, TN, CA, KY, VI, IL, WI,MS, UT, CO, ND") +
		  theme(plot.title = element_text(size = 10, face = "bold"), axis.title=element_text(size=14,face="bold")) +
		  xlab("STORM EVENT TYPE") +
              theme(axis.title.y = element_text(size = rel(0.5), angle = 90), axis.title=element_text(size = 14, face = "bold")) +
		  theme(axis.title.x = element_text(size = rel(0.5), angle = 0), axis.title=element_text(size=14,face="bold")) +
		  annotation_custom(tableGrob(round(statsa, digits = 3), theme=ttheme_minimal(base_size = 7)))

Plot 2 graphs on the same panel

grid.arrange(p1, p2)

2

When you knit an Rmd document, the process is done in a fresh session, so you are correct in saying that df_max would not be found.

You therefore need to include a code chunk within your Rmd file that imports the data used within the document.

3

Thank you. What Knitr chunk wouldI use to import the
data withing the document?

4

You could use one single chunk to do all your data import, after your chunk where you load all the packages you'll be using. For example:

```{r setup, include = FALSE}
library(dplyr)
library(readr)
library(ggplot2)
```

```{r data-import, include = FALSE}
data_max <- # whatever you do to import data_max

cost1a_max  <- # whatever you do to import cost1a_max
```

The rest of your document here
5

So, let's say that i read data from a file, ex; data <- read.table.................
after that, I can write

the ```{r data_import,.........}
data_max <- data
cost1_max <- data

Is that how is done?

6

Correct, so it might look like

```{r data-import, include = FALSE} 
data_max <- read.table(# your arguments here)
cost1a_max <- read.table(# your arguments here)
```
7

Yes, that works, now the graph can access the data.
I have another problem. I have to display 3 panels with different data for each graph in the panel - please see below - and I only get to display the first one. Also the first panel is repeated. How should I do this? I guess the question is: Is there any thing I can do to overwrite file.png. If I use different file names in each chung, ie; file.png, file1.png, file2.png the program halts with an error.

file1.png cannot be found. This is very strange becuause each graph invokes a different data frame.

dev.new(width =20000, height = 10000, unit = "px")

 knitr::include_graphics("C:/Users/giuse/OneDrive/Documents/DataScience/R SCRIPTS/STORM DATA/file.png", auto_pdf = getOption("knitr.graphics.auto_pdf", FALSE),dpi = NULL)

Here are there are 3 ggplot panels:
p1 <- ggplot(...........)

p2 <- ggplot(............)

arrange(p1,p2)

dev.new(width =20000, height = 10000, unit = "px")

 knitr::include_graphics("C:/Users/giuse/OneDrive/Documents/DataScience/R SCRIPTS/STORM DATA/file.png", auto_pdf = getOption("knitr.graphics.auto_pdf", FALSE),dpi = NULL)

p3 <- ggplot(........)
p4 <- ggplot(........)
arrange(p2,p3)

dev.new(width =20000, height = 10000, unit = "px")

 knitr::include_graphics("C:/Users/giuse/OneDrive/Documents/DataScience/R SCRIPTS/STORM DATA/file.png", auto_pdf = getOption("knitr.graphics.auto_pdf", FALSE),dpi = NULL)
p5 <- ggplot(.......)
p6 <- ggplot(.......)
arrange(p5,p6)
8

This is the solution with library(plotly)

Initialize device

dev.new(width =20000, height = 10000, unit = "px")

library(plotly)
# Plot the event types that cause the largest number of injuries across all the states in the USA. Include the summary statistics table on the graph
p1 <- ggplot(df_max, aes(EVTYPE, INJURIES)) + geom_point(color = "blue") + theme(legend.position="top") + 
 		  theme(axis.text.x = element_text(color = "grey20", size = 7.0, angle = 90, hjust = .5, vjust = .5, face = "plain"),     
   		  axis.text.y = element_text(color = "grey20", size = 5, angle = 50, hjust = 0.5, vjust = 0, face = "plain")) +
              ggtitle("Health Inpact - INJURIES - of Severe Storms Across the USA") +
		  theme(plot.title = element_text(size = 10, face = "bold")) +
		  xlab("STORM EVENT TYPE") +
		  theme(axis.title.y = element_text(size = rel(0.5), angle = 90), axis.title=element_text(size=14,face="bold")) +
    		  theme(axis.title.x = element_text(size = rel(0.5), angle = 0), axis.title=element_text(size=14,face="bold")) +
              annotation_custom(tableGrob(round(stats, digits = 3), theme=ttheme_minimal(base_size = 7)))


# Plot the events causing the maximum amount of property damage across cost1a states. Include the summary statistics table on the graph.
p2 <- ggplot(cost1a_max, aes(EVTYPE, PROPDMG)) + geom_point(color = "blue") + theme(legend.position="top") + 
 		  theme(axis.text.x = element_text(color = "grey20", size = 7.0, angle = 90, hjust = .5, vjust = .5, face = "plain"),     
  		  axis.text.y = element_text(color = "grey20", size = 5, angle = 50, hjust = 0.5, vjust = 0, face = "plain")) +
              ggtitle("Economic Inpact - PROPERTY DAMAGE - of Severe Storms across the states of GU, TX, AK, TN, CA, KY, VI, IL, WI,MS, UT, CO, ND") +
		  theme(plot.title = element_text(size = 10, face = "bold"), axis.title=element_text(size=14,face="bold")) +
		  xlab("STORM EVENT TYPE") +
              theme(axis.title.y = element_text(size = rel(0.5), angle = 90), axis.title=element_text(size = 14, face = "bold")) +
		  theme(axis.title.x = element_text(size = rel(0.5), angle = 0), axis.title=element_text(size=14,face="bold")) +
		  annotation_custom(tableGrob(round(statsa, digits = 3), theme=ttheme_minimal(base_size = 7))) 


# Plot 2 graphs on the same panel
grid.arrange(p1, p2)
1 Like
9

How can I include a command to display the code and code results inside an import command/

data_max <- read.table(# your arguments here)
cost1a_max <- read.table(# your arguments here)
10

I guess the question is, is there a command to display all the code and code results globally? I have tried the command below but it does not work

knitr::opts_chunk$set(echo = TRUE)
11

The solution is

```{r data-import, include = TRUE}
12

This topic was automatically closed 7 days after the last reply. New replies are no longer allowed.