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support more than 6 replicates #20 #35

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8 changes: 7 additions & 1 deletion R/pca.R
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Original file line number Diff line number Diff line change
Expand Up @@ -64,7 +64,7 @@
#' @seealso \code{\link{plot_correlation_heatmap}}
#'
#' @importFrom ggplot2 ggplot aes geom_point labs theme_bw theme element_blank
#' element_line facet_wrap geom_text
#' element_line facet_wrap geom_text scale_shape_manual
#' @importFrom plotly plot_ly add_trace layout
#' @importFrom SummarizedExperiment assay colData metadata
#' @importFrom dplyr left_join select
Expand Down Expand Up @@ -338,6 +338,8 @@ plot_pca <- function(dep, x = 1, y = 2, indicate = c("condition", "replicate"),
}
}
} else { # static plot by ggplot2
shape_palette <- c(16, 17, 15, 3, 7, 8, 0, 1, 2, 4, 5, 6, 9, 10, 11, 12, 13, 14, 18, 20, 21, 22, 23, 24, 25, 19)

p <- ggplot(pca_df, aes(get(paste0("PC", x)), get(paste0("PC", y)))) +
labs(
title = paste0("PCA plot - top ", n, " variable features"),
Expand All @@ -358,26 +360,30 @@ plot_pca <- function(dep, x = 1, y = 2, indicate = c("condition", "replicate"),
labs(col = indicate[1])
}
if (length(indicate) == 2) {
n_shapes <- nlevels(pca_df[[indicate[2]]])
p <- p + geom_point(
aes(
col = pca_df[[indicate[1]]],
shape = pca_df[[indicate[2]]]
),
size = point_size
) +
scale_shape_manual(values = shape_palette[seq_len(n_shapes)]) +
labs(
col = indicate[1],
shape = indicate[2]
)
}
if (length(indicate) == 3) {
n_shapes <- nlevels(pca_df[[indicate[2]]])
p <- p + geom_point(
aes(
col = pca_df[[indicate[1]]],
shape = pca_df[[indicate[2]]]
),
size = point_size
) +
scale_shape_manual(values = shape_palette[seq_len(n_shapes)]) +
facet_wrap(~ pca_df[[indicate[3]]])
labs(
col = indicate[1],
Expand Down
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