R/graph_prots.R

In EliLillyCo/surfaltr: Rapid Comparison of Surface Protein Isoform Membrane Topologies Through surfaltr

#' Create a plot showing where each amino acid is located within the cell for
#' each primary transcript compared to each alternative transcript
#'
#' This function creates a ggplot figure showing the differences in membrane
#' location and length between primary and alternative transcripts from the
#' same gene. Transcripts derived from the same gene are grouped together
#' to facilitate easy interpretation. The y axis lists the gene name and
#' transcript ID for each transcript and the x axis lists the length in
#' amino acids. Each fill color corresponds to a membrane location and either
#' principal or alternative isoform.
#'
#' @usage graph_prots(counts, rank = "length", n_prts = 20, size_txt = 2,
#' space_left = -400)
#' @param counts A data frame containing the overall length and individual 
#' lengths of each section of the surface protein corresponding to a certain 
#' transcript.
#' @param rank String indicating which method to use to rank proteins in graphical
#' output. Options include "Length", "TM", and "Combo".
#' @param n_prts Integer value indicating the number of genes that should be
#' displayed on the graphical output. Default value is 20.
#' @param size_txt Integer value specifying the size of the row labels. Default
#' size is 2.
#' @param space_left Integer value specifying how far left the graph should
#' extend.
#' @import ggplot2
#' @return A ggplot figure showing the protein locations for each part of the
#' surface protein for each alternative and primary transcripts.
#'


graph_prots <- function(counts, rank = "length", n_prts = 20, size_txt = 2, 
    space_left = -400) {
    counts <- rank_prts(counts, rank, n_prts)
    counts$Order <- as.numeric(counts$Order)
    counts$Begin <- as.numeric(counts$Begin)
    counts$End <- as.numeric(counts$End)
    Begin <- End <- Order <- NULL
    cols <- c()
    p <- ggplot2::ggplot()
    p <- p + ggplot2::ylim(0.5, max(counts$Order) + 0.5)
    p <- p + ggplot2::xlim(
        space_left,
        max(counts$End) + max(counts$End) * 0.1
    )
    p <- p + ggplot2::labs(x = "Amino Acid Number")
    p <- p + ggplot2::labs(y = "Transcript ID")
    p <- p + ggplot2::annotate("text",
    x = -10,
    y = counts[counts$Membrane_Location != "M" | counts$Membrane_Location != "O" |
    counts$Membrane_Location != "o" | counts$Membrane_Location != "i", ]$Order,
    label = paste(counts$Gene_Name, counts$Transcript_ID, sep = "; "),
    hjust = 1,
    size = size_txt
    )
    if (nrow(counts[counts$Membrane_Location == "M" & 
        substr(counts$APPRIS_Annotation, 1, 2) == "pr", ]) != 0) {
        p <- p + ggplot2::geom_rect(
            data = counts[counts$Membrane_Location == "M" &
                substr(counts$APPRIS_Annotation, 1, 2) == "pr", ],
            ggplot2::aes(
                xmin = as.numeric(Begin),
                xmax = as.numeric(End),
                ymin = as.numeric(Order) - 0.2,
                ymax = as.numeric(Order) + 0.2,
                fill = "M, Pr",
            ),
            size = 0.1,
        )
        cols <- append(cols, "#004754")
    }
    if (nrow(counts[counts$Membrane_Location == "M" & 
        (substr(counts$APPRIS_Annotation, 1, 2) == " _" |
        substr(counts$APPRIS_Annotation, 1, 2) == "al" |
        substr(counts$APPRIS_Annotation, 1, 2) == "NA"), ]) != 0) {
        p <- p + ggplot2::geom_rect(
            data = counts[counts$Membrane_Location ==
                "M" & (substr(counts$APPRIS_Annotation, 1, 2) == " _" |
                substr(counts$APPRIS_Annotation, 1, 2) == "al" |
                substr(counts$APPRIS_Annotation, 1, 2) == "NA"), ],
            ggplot2::aes(
                xmin = as.numeric(Begin),
                xmax = as.numeric(End),
                ymin = as.numeric(Order) - 0.2,
                ymax = as.numeric(Order) + 0.2,
                fill = "M, Alt"
            ),
            size = 0.1
        )
        cols <- append(cols, "#540000")
    }
    if (nrow(counts[(counts$Membrane_Location == "O" | 
        counts$Membrane_Location == "o") &
        substr(counts$APPRIS_Annotation, 1, 2) == "pr", ]) != 0) {
        p <- p + ggplot2::geom_rect(
            data = counts[(counts$Membrane_Location == "O" |
                counts$Membrane_Location == "o") &
                substr(counts$APPRIS_Annotation, 1, 2) == "pr", ],
            ggplot2::aes(
                xmin = as.numeric(Begin),
                xmax = as.numeric(End),
                ymin = as.numeric(Order) - 0.2,
                ymax = as.numeric(Order) + 0.2,
                fill = "O, Pr"
            ),
            size = 0.1
        )
        cols <- append(cols, "#ABC3C9")
    }
    if (nrow(counts[(counts$Membrane_Location == "O" | 
    counts$Membrane_Location == "o") &
    (substr(counts$APPRIS_Annotation, 1, 2) == " _" | 
    substr(counts$APPRIS_Annotation, 1, 2) == "al" | 
    substr(counts$APPRIS_Annotation, 1, 2) == "NA"), ]) != 0) {
        p <- p + ggplot2::geom_rect(
            data = counts[(counts$Membrane_Location == "O" |
                counts$Membrane_Location == "o") &
                (substr(counts$APPRIS_Annotation, 1, 2) == " _" |
                    substr(counts$APPRIS_Annotation, 1, 2) == "al" |
                    substr(counts$APPRIS_Annotation, 1, 2) == "NA"), ],
            ggplot2::aes(
                xmin = as.numeric(Begin),
                xmax = as.numeric(End),
                ymin = as.numeric(Order) - 0.2,
                ymax = as.numeric(Order) + 0.2,
                fill = "O, Alt"
            ),
            size = 0.1
        )
        cols <- append(cols, "#63ACBE")
    }
    if (nrow(counts[counts$Membrane_Location == "i" & 
        substr(counts$APPRIS_Annotation, 1, 2) == "pr", ]) != 0) {
        p <- p + ggplot2::geom_rect(
            data = counts[counts$Membrane_Location == "i" &
                substr(counts$APPRIS_Annotation, 1, 2) == "pr", ],
            ggplot2::aes(
                xmin = as.numeric(Begin),
                xmax = as.numeric(End),
                ymin = as.numeric(Order) - 0.2,
                ymax = as.numeric(Order) + 0.2,
                fill = "i, Pr"
            ),
            size = 0.1
        )
        cols <- append(cols, "#B5D99C")
    }
    if (nrow(counts[counts$Membrane_Location == "i" & 
        (substr(counts$APPRIS_Annotation, 1, 2) == " _" |
        substr(counts$APPRIS_Annotation, 1, 2) == "al" |
        substr(counts$APPRIS_Annotation, 1, 2) == "NA"), ]) != 0) {
        p <- p + ggplot2::geom_rect(
            data = counts[counts$Membrane_Location == "i" &
                (substr(counts$APPRIS_Annotation, 1, 2) == " _" |
                    substr(counts$APPRIS_Annotation, 1, 2) == "al" |
                    substr(counts$APPRIS_Annotation, 1, 2) == "NA"), ],
            ggplot2::aes(
                xmin = as.numeric(Begin),
                xmax = as.numeric(End),
                ymin = as.numeric(Order) - 0.2,
                ymax = as.numeric(Order) + 0.2,
                fill = "i, Alt"
            ),
            size = 0.1
        )
        cols <- append(cols, "#EE442F")
    }
    if (nrow(counts[counts$Membrane_Location == "S" & 
        substr(counts$APPRIS_Annotation, 1, 2) == "pr", ]) != 0) {
        p <- p + ggplot2::geom_rect(
            data = counts[counts$Membrane_Location == "S" &
                substr(counts$APPRIS_Annotation, 1, 2) == "pr", ],
            ggplot2::aes(
                xmin = as.numeric(Begin),
                xmax = as.numeric(End),
                ymin = as.numeric(Order) - 0.2,
                ymax = as.numeric(Order) + 0.2,
                fill = "S, Pr",
            ),
            size = 0.1,
        )
        cols <- append(cols, "#FDB261")
    }
    if (nrow(counts[counts$Membrane_Location == "S" & 
        (substr(counts$APPRIS_Annotation, 1, 2) == " _" |
        substr(counts$APPRIS_Annotation, 1, 2) == "al" |
        substr(counts$APPRIS_Annotation, 1, 2) == "NA"), ]) != 0) {
        p <- p + ggplot2::geom_rect(
            data = counts[counts$Membrane_Location == "S" &
                (substr(counts$APPRIS_Annotation, 1, 2) == " _" |
                    substr(counts$APPRIS_Annotation, 1, 2) == "al" |
                    substr(counts$APPRIS_Annotation, 1, 2) == "NA"), ],
            ggplot2::aes(
                xmin = as.numeric(Begin),
                xmax = as.numeric(End),
                ymin = as.numeric(Order) - 0.2,
                ymax = as.numeric(Order) + 0.2,
                fill = "S, Alt"
            ),
            size = 0.1
        )
        cols <- append(cols, "#B3A78C")
    }
    p <- p + ggplot2::theme_light()
    p <- p + ggplot2::theme(axis.text.y = ggplot2::element_blank())
    p <- p + ggplot2::theme(legend.text = ggplot2::element_text(size = 10))
    p <- p + ggplot2::theme(
        axis.text = ggplot2::element_text(size = 15),
        axis.title = ggplot2::element_text(size = 15)
    )
    cols <- as.data.frame(cols)
    colnames(cols) <- "colors"
    order_col <- as.data.frame(c(
        "#EE442F", "#B5D99C", "#540000", "#004754", "#63ACBE",
        "#ABC3C9", "#FDB261", "#B3A78C"
    ))
    colnames(order_col) <- "colors"
    order_col$ord <- seq_len(nrow(order_col))
    col_corr <- merge(x = cols, y = order_col, by = "colors")
    col_corr <- col_corr[order(col_corr$ord), ]
    fin_col <- as.vector(col_corr$colors)
    p <- p + ggplot2::scale_fill_manual(name = "", values = fin_col)
    p
    return(p)
}