## ---- include = FALSE--------------------------------------------------------- rmarkdown.html_vignette.check_title = FALSE library(devtools) devtools::load_all() library(knitr) library(kableExtra) ## ---- eval = FALSE------------------------------------------------------------ # if (!require("BiocManager", quietly = TRUE)) # install.packages("BiocManager") # # BiocManager::install("surfaltr") ## ---- eval = FALSE------------------------------------------------------------ # library(surfaltr) ## ---- eval = FALSE------------------------------------------------------------ # check_tmhmm_install(path/to/folder/TMHMM2.0c) ## ---- echo = FALSE, out.width = "85%", fig.align = "center"------------------- knitr::include_graphics("Figure_1.png") ## ---- eval=FALSE-------------------------------------------------------------- # graph_from_aas(data_file = system.file("extdata", "CRB1.csv", package="surfaltr"), # organism = "mouse", rank = "combo", # n_prts = 20, mode = "phobius", size_txt = 2, space_left = -400, # temp = FALSE) # # graph_from_ids(data_file = system.file("extdata", "hpa_genes.csv",package="surfaltr"), # organism = "human", # rank = "combo", n_prts = 20, mode = "phobius", size_txt = 2, # space_left = -400, temp = FALSE) ## ---- echo = FALSE------------------------------------------------------------ all_genome_data <- read.csv(file = "hpa_genes.csv", header = TRUE) kable(head(all_genome_data), align = 'c')%>% kable_styling(full_width = TRUE) ## ---- echo = FALSE------------------------------------------------------------ all_genome_data <- read.csv(file = "CRB1.csv", header = TRUE) all_genome_data <- data.frame(lapply(all_genome_data, substr, 1, 70)) for(row in 1:nrow(all_genome_data)){ all_genome_data[row, "protein_sequence"] <- paste(all_genome_data[row, "protein_sequence"], "...", sep = "") } kable(head(all_genome_data), align = 'c')%>% kable_styling(full_width = TRUE) ## ---- echo = FALSE------------------------------------------------------------ inp <- read.csv(file = "Input_Table.csv", header = TRUE, fileEncoding="latin1") kable(inp, align = 'c')%>% kable_styling(full_width = TRUE) ## ---- eval=FALSE------------------------------------------------------------- # graph_from_ids(data_file = system.file("extdata", "hpa_genes.csv",package="surfaltr"), organism = "human", # rank = "combo", n_prts = 20, mode = "phobius", size_txt = 2, # space_left = -400, tmhmm_folder_name = NULL) ## ---- eval=FALSE-------------------------------------------------------------- # graph_from_aas(data_file = system.file("extdata", "CRB1.csv", package="surfaltr"), organism = "mouse", rank = "TM", # n_prts = 10, mode = "phobius", size_txt = 2, space_left = -400, # tmhmm_folder_name = NULL) # ## ---- eval = FALSE------------------------------------------------------------ # AA_seq <- get_pairs(data_file = system.file("extdata", "CRB1.csv", package="surfaltr"), if_aa = TRUE, organism = "mouse", temp = FALSE) # ## ---- echo = FALSE, out.width = "200%", fig.align = "center"------------------ knitr::include_graphics("crb1_output.PNG") ## ---- echo = FALSE, fig.align = "center"-------------------------------------- knitr::include_graphics("CRB1_fasta_ss.PNG") ## ---- echo = FALSE, out.width = "50%", fig.align = "center"------------------- knitr::include_graphics("Figure_2.png") ## ---- eval = FALSE------------------------------------------------------------ # mem_topo <- get_tmhmm(fasta_file_name = "AA.fasta", tmhmm_folder_name = "~/path/to/TMHMM2.0c") ## ---- eval = FALSE------------------------------------------------------------ # AA_lst <- get_pairs(data_file = system.file("extdata", "CRB1.csv", package="surfaltr"), if_aa = TRUE, organism = "mouse") # mem_topo <- get_tmhmm("AA.fasta", tmhmm_folder_name = "~/path/to/TMHMM2.0c") ## ---- eval = FALSE------------------------------------------------------------ # topo <- run_phobius(AA_seq = AA_lst, fasta_file_name = "~//output/AA.fasta") ## ---- eval = FALSE------------------------------------------------------------ # AA_lst <- get_pairs(data_file = "~/CRB1.csv", if_aa = TRUE, organism = "mouse") # mem_topo <- run_phobius(AA_seq = AA_lst, fasta_file_name = "~//output/AA.fasta") ## ---- eval = FALSE------------------------------------------------------------ # AA_lst <- get_pairs(data_file = system.file("extdata", "CRB1.csv", package="surfaltr"), if_aa = TRUE, organism = "mouse") # mem_topo <- run_phobius(AA_seq = AA_lst, fasta_file_name = "~//AA.fasta") # plot_isoforms(topo = mem_topo, AA_seq = AA_lst, rank = "combo", n_prts = 15, # size_txt = 3, space_left = -400) ## ---- echo = FALSE------------------------------------------------------------ tm_rank <- read.csv(file = "TM_Table.csv", header = TRUE, fileEncoding="latin1") kable(tm_rank, align = 'c')%>% kable_styling(full_width = FALSE) ## ---- echo = FALSE------------------------------------------------------------ cm_rank <- read.csv(file = "Combo_Table.csv", header = TRUE, fileEncoding="latin1") kable(cm_rank, align = 'c')%>% kable_styling(full_width = FALSE) ## ---- echo = FALSE, out.width = "65%", fig.align = "center"------------------- knitr::include_graphics("Figure_3.png") ## ---- echo = FALSE------------------------------------------------------------ ft_rank <- read.csv(file = "Format_Table.csv", header = TRUE, fileEncoding="latin1") kable(ft_rank, align = 'c')%>% kable_styling(full_width = TRUE) ## ---- echo = FALSE, out.width = "50%", fig.align = "center"------------------- knitr::include_graphics("Figure_4.png") ## ---- eval = FALSE------------------------------------------------------------ # align_prts(gene_names = c("Crb1", "Adgrl1"), data_file = system.file("extdata", "CRB1.csv", package="surfaltr"), # if_aa = TRUE, organism = "mouse") ## ---- eval = FALSE------------------------------------------------------------ # align_org_prts(gene_names = c("gene-name"), hs_data_file = "~/path/to/human-dataframe.csv", # mm_data_file = "~/path/to/mouse-dataframe.csv", if_aa = FALSE) ## ---- echo = FALSE, fig.align = "center"-------------------------------------- knitr::include_graphics("Figure_5.png") ## ---- eval = FALSE------------------------------------------------------------ # library(surfaltr) ## ---- eval = TRUE------------------------------------------------------------- sessionInfo() ## ---- include = FALSE--------------------------------------------------------- knitr::opts_chunk$set( collapse = TRUE, comment = "#>" ) ## ----setup, include = FALSE--------------------------------------------------- library(surfaltr)