r - ggplot2 plotting with black outline -

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i cross posting forum (https://www.biostars.org/p/268514/#268559) got useful comments still confused output of ggplot2.

i trying simple black outline on circles code giving random colours , seems ignoring scale_colour_manual(values = cols) argument. when run following code:

# creating color palette  > cols <- c("red" = "red", "orange" = "orange", "nonsignificant" = "darkgrey", "increased" = "#00b2ff", "decreased" = "#00b2ff")  # make basic ggplot2 object  > vol <- ggplot(data, aes(x = lfc, y = pval, color = color, labels=gene))  # inserting mnaual colors per color pallette  term "scale_colour_manual(values = cols)" below  > vol +      ggtitle(label = "volcano plot", subtitle = "colored fold-change direction") +   geom_point(size = 2.5, alpha = 1, na.rm = t) +   scale_colour_manual(values = cols) +   theme_bw(base_size = 14) +    theme(legend.position = "right") +    xlab(expression(log[2]("vitd" / "carrier"))) +    ylab(expression(-log[10]("fdr"))) + # change y-axis label   geom_hline(yintercept = 1, colour="#990000", linetype="dashed") + geom_vline(xintercept = 0.586, colour="#990000", linetype="dashed") + geom_vline(xintercept = -0.586, colour="#990000", linetype="dashed") +    scale_y_continuous(trans = "log1p")

i beautiful graph defined colour palette:

color volcano plot

next, want add border points , change 2 pieces of code. @ start make basic ggplot object "fill = color" instead of "color = color"

> vol <- ggplot(data, aes(x = lfc, y = pval, fill = color, labels=gene))

and add "shape = 21, colour = "black"" "geom_point" argument:

> vol +      ggtitle(label = "volcano plot", subtitle = "colored fold-change direction") +   geom_point(size = 2.5, alpha = 1, na.rm = t, shape = 21, colour = "black") +   scale_colour_manual(values = cols) +   theme_bw(base_size = 14) +    theme(legend.position = "right") +    xlab(expression(log[2]("vitd" / "carrier"))) +    ylab(expression(-log[10]("fdr"))) + l   geom_hline(yintercept = 1, colour="#990000", linetype="dashed") + geom_vline(xintercept = 0.586, colour="#990000", linetype="dashed") + geom_vline(xintercept = -0.586, colour="#990000", linetype="dashed") +    scale_y_continuous(trans = "log1p")

and have plot seems random selection of 5 colours; , if print colors:

print(cols)  red      orange         nonsignificant      increased      decreased  "red"    "orange"      "darkgrey"           "#00b2ff"      "#00b2ff"

the palette still there.

when change color = cols fill = cols, should change scale_color_manual(...) scale_fill_manual(...)





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