From e85a9c888ce2cce7115e0dd9d665e964ce512a28 Mon Sep 17 00:00:00 2001 From: Daniel Park Date: Fri, 8 Dec 2023 15:12:26 -0500 Subject: [PATCH] fix image url, format code --- README.md | 10 ++++++---- 1 file changed, 6 insertions(+), 4 deletions(-) diff --git a/README.md b/README.md index 47589af..d93216b 100644 --- a/README.md +++ b/README.md @@ -32,8 +32,10 @@ After you have installed `reconstructR`, you will need to assemble the data that - This should be a csv file where the first column is titled \texttt{position} and each subsequent column is titled with the exact name of all genomic sequences in the `aligned.fasta` file. The `position` column should then have entries from 1 to the full length of the reference genome. Each subsequent column should then contain the sequencing read depth of the column's genome at the indicated position. - For example if `aligned.fasta` contained three genomes named `genome_1`, `genome_2`, `genome_3` then `depth.csv` should look like: ``` - depth = data.frame(position=1:29903,genome_1=round(rnorm(29903,50,10)),genome_2=round(rnorm(29903,100,10)), - genome_3=round(rnorm(29903,70,10))) + depth = data.frame(position=1:29903, + genome_1=round(rnorm(29903,50,10)), + genome_2=round(rnorm(29903,100,10)), + genome_3=round(rnorm(29903,70,10))) print(head(depth)) print(tail(depth)) ``` @@ -41,7 +43,7 @@ After you have installed `reconstructR`, you will need to assemble the data that - This should be a csv file where the first column contains the exact name of all genomic sequences in the `aligned.fasta` file and the second column contains the number of days between the collection date of each sample and the earliest collected sample. - For example if `aligned.fasta` contained three genomes named `genome_1`, `genome_2`, `genome_3` where `genome_1` was tested first, then `date.csv` should look like: ``` - date = data.frame(col1=c("genome_1","genome_2","genome_3"),col2=c(0,2,4)) + date = data.frame(col1=c("genome_1","genome_2","genome_3"), col2=c(0,2,4)) print(date) ``` - A folder called `vcf` @@ -54,7 +56,7 @@ After you have installed `reconstructR`, you will need to assemble the data that Finally, in the directory that you created `input_data` create a new R script, which is where you will run and analyze `reconstructR`. The overall file structure should look as follows: -![File Structure]("man/file_structure.png") +![File Structure](man/file_structure.png) ## Running `reconstructR`