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@@ -50,7 +50,7 @@
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50
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#' viz_pwm(pwm_mat = pwm, method = "bits", fixed_coord = TRUE)
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#'
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viz_pwm <- function(pwm_mat, method = "heatmap", pos_lab = NULL,
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53
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- pdf_name = NULL, fixed_coord = FALSE, bits_yax = "full"){
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+ pdf_name = NULL, fixed_coord = FALSE, bits_yax = "full"){
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pos_lab <- set_default_pos_lab2(pwm_mat, pos_lab)
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check_vars(pwm_mat, pos_lab)
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...
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@@ -61,7 +61,7 @@ viz_pwm <- function(pwm_mat, method = "heatmap", pos_lab = NULL,
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pwm_mat_df$Nucleotides <- rownames(pwm_mat_df)
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colnames(pwm_mat_df) <- c(pos_lab, "Nucleotides")
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pwm_mat_df_for_ggheatmap <- melt(pwm_mat_df, id.vars = c("Nucleotides"),
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64
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- variable.name = "positions")
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+ variable.name = "positions")
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p1 <- get_ggheatmap(pwm_mat_df = pwm_mat_df_for_ggheatmap)
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}else{
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p1 <- get_ggseqlogo(pwm_mat, method = method, pos_lab = pos_lab)
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...
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@@ -91,13 +91,13 @@ get_ggheatmap <- function(pwm_mat_df){
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ggplot2::theme_bw() +
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ggplot2::xlab(label = element_blank()) +
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ggplot2::scale_fill_gradient2(name = "", low = "white",
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- mid = "white", high = "#012345") +
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+ mid = "white", high = "#012345") +
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ggplot2::theme(legend.position = "top",
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96
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- legend.justification = "center",
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97
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- legend.margin = margin(0,-1,0,0),
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98
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- axis.text.x = element_text(size = rel(0.8), angle = 90,
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- hjust = 1, vjust = 0.5),
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- plot.margin = margin(0,0,0,0)
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+ legend.justification = "center",
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+ legend.margin = margin(0,-1,0,0),
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+ axis.text.x = element_text(size = rel(0.8), angle = 90,
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+ hjust = 1, vjust = 0.5),
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+ plot.margin = margin(0,0,0,0)
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)
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##
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p1
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