Why does my code chunk render my plot correctly when run by itself but I get an 'object not found' error when I try to knit in R Markdown? - r-markdown

Question

I am relatively new at R Markdown and am having trouble when trying to knit to create a report. The error I am getting is:
Error in ggplot(data = bio1530_sci1420_summary_stats.xlsx) :
object 'bio1530_sci1420_summary_stats.xlsx' not found
Calls: ... withVisible -> eval_with_user_handlers -> eval -> eval -> ggplot
Execution halted
Here is my code thus far:
title: "NGRMarkdown"
author: "Rob McCandless"
date: "r Sys.Date()"
output: word_document
knitr::opts_chunk$set(echo = TRUE)
library(ggplot2)
library(ggrepel)
library(tidyverse)
library(here)
read_csv("bio1530_sci1420_summary_stats.xlsx")
#ScatterPlot of mean course grade v. mean normalized gain on 1420 and 1530 data with regression lines and error bars
ggplot(data=bio1530_sci1420_summary_stats.xlsx)+
geom_errorbar(aes(x=Course_grade, y=Norm_gain, ymin=Norm_gain-CI, ymax=Norm_gain+CI), color="black", width=0.2, position=position_dodge2(10.0))+
geom_point(mapping=aes(x=Course_grade, y=Norm_gain, shape=Course, color=Course),size=3)+
geom_smooth(method=lm, se=FALSE, col='black', size=1, mapping=aes(x=Course_grade, y=Norm_gain, linetype=Course))+
geom_label_repel(aes(Course_grade, y=Norm_gain, label = Alpha), box.padding = 0.3, point.padding = 0.7, segment.color = 'grey50')+ #added point labels A-J
ylab('Mean Normalized Gain (all instructor sections)')+
xlab('Mean Course Grade (all instructor sections)')+
scale_fill_discrete(labels=c("Bio 1530", "Sci 1420"))+
labs(title="Normalized Gain v. Course Grade by Course & Instructor", subtitle="Mean and 95% CI of all sections per instructor (A-J)")+
theme(plot.title=element_text(hjust=0.5))+
theme(plot.subtitle=element_text(hjust=0.5))+
annotate("text", x=73.0, y=0.09, label="R2 = 0.68, p = 0.044")+
annotate("text", x=78.5, y=0.22, label="R2 = 0.46, p = 0.095")
And this is the plot that renders when I tell R to run this chunk only:
[Course grade v. normalized gain](https://i.stack.imgur.com/WO9S7.png)
So the code works and the dataframe the code refers to is valid, but it won't render when I try to knit in R Markdown.
I suspect it may have to do with the current and working directories not being the same, but I'm not certain of this and am not sure how to check this. I have confirmed that my my working directory is:
getwd()
[1] "/Users/robmccandless/Library/Mobile Documents/com~apple~CloudDocs/R Projects/Normalized_Gain_Data"
and this is where the dataframe and RMD file are both located. Can anyone give me some idea of what I am doing wrong? Any assistance will be greatly appreciated.

Answer 1

the error is saying that your dataset object (i.e., the .xlsx file) is not found in the your local environment. From snippet above it doesn't look like the dataset is saved, just read. One option is to try in your markdown:
df <- read_csv("bio1530_sci1420_summary_stats.xlsx")
ggplot(data=df)+
geom_errorbar(aes(x=Course_grade, y=Norm_gain, ymin=Norm_gain-CI, ymax=Norm_gain+CI), color="black", width=0.2, position=position_dodge2(10.0))+
geom_point(mapping=aes(x=Course_grade, y=Norm_gain, shape=Course, color=Course),size=3)+
geom_smooth(method=lm, se=FALSE, col='black', size=1, mapping=aes(x=Course_grade, y=Norm_gain, linetype=Course))+
geom_label_repel(aes(Course_grade, y=Norm_gain, label = Alpha), box.padding = 0.3, point.padding = 0.7, segment.color = 'grey50')+ #added point labels A-J
ylab('Mean Normalized Gain (all instructor sections)')+
xlab('Mean Course Grade (all instructor sections)')+
scale_fill_discrete(labels=c("Bio 1530", "Sci 1420"))+
labs(title="Normalized Gain v. Course Grade by Course & Instructor", subtitle="Mean and 95% CI of all sections per instructor (A-J)")+
theme(plot.title=element_text(hjust=0.5))+
theme(plot.subtitle=element_text(hjust=0.5))+
annotate("text", x=73.0, y=0.09, label="R2 = 0.68, p = 0.044")+
annotate("text", x=78.5, y=0.22, label="R2 = 0.46, p = 0.095")