ggpubr

Lay out multiple ggplot graphs on a page

由 落花浮王杯 提交于 2020-01-16 09:51:30
问题 I generate a list of ggplot objects inside a loop as follows: myPlots = list() for(i in 1:length(maturities)){ myPlots[[i]] <- ggplot(deltaIR.df, aes(sample = deltaIR.df[,i])) + stat_qq() + stat_qq_line() + labs(title=maturities[i], x = "Theoretical (Normal)", y = "Empirical Distribution") } Depending on the dataset, there could be between 4 and 10 plots in myPlots. I now want to print them on one page in two rows, and have tried various methods with varying degrees of success. The most

Use dataframe variable names in plot titles

由 旧街凉风 提交于 2019-12-29 09:28:27
问题 I have a dataframe with several variables that I wish to label and then use in several ggplots. I have applied labels using the labeller package with the following code. library(tidyverse) library(labeller) library(ggpubr) example.df <- data.frame( origin = sample(c("hum_1", "mou_1"), 100, replace = TRUE), v1 = rnorm(100, 100, 5), v2 = rnorm(100, 10,5), v3 = rnorm (100, 25, 5)) example.df <- example.df %>% set_variable_labels(origin = "original sample", v1 = "effect of Rx", v2 = "response",

R ggplot2 boxplots - ggpubr stat_compare_means not working properly

由 落爺英雄遲暮 提交于 2019-12-28 16:13:28
问题 I am trying to add significance levels to my boxplots in the form of asterisks using ggplot2 and the ggpubr package, but I have many comparisons and I only want to show the significant ones. I try to use the option hide.ns=TRUE in stat_compare_means , but it clearly does not work , it might be a bug in the ggpubr package. Besides, you see that I leave out group "PGMC4" from the pairwise wilcox.test comparisons; how can I leave this group out also for the kruskal.test ? The last question I

add mean value on boxplot with ggpubr

由 怎甘沉沦 提交于 2019-12-13 03:03:18
问题 I'm trying to add a label on boxplot using ggpubr package. Here's the code I used: library(ggplot2) library(ggpubr) compare_means(len ~ supp, data = ToothGrowth, method="t.test", paired=TRUE, group.by = "dose") # Box plot facetted by "dose" p1 <- ggboxplot(ToothGrowth, x = "supp", y = "len", xlab=F, color = "supp", palette = "jco", facet.by = "dose", add="mean", short.panel.labs = FALSE) # Use only p as label. p2 <- p1 + stat_compare_means(method = "t.test", paired = T, label = "p") p2 And

how can I add multiple pvalues to ggplot grouped boxplot

由 浪尽此生 提交于 2019-12-11 04:13:45
问题 I have boxplot and I would like to add pvalues for 4 comparisons across two factors. Here is the data set: dput(CauloQ_datMannot) structure(list(V1 = structure(c(1L, 1L, 1L, 2L, 2L, 2L, 3L, 3L, 3L, 4L, 4L, 4L), .Label = c("B", "BF", "BFi ", "Bi"), class = "factor"), variable = structure(c(1L, 2L, 3L, 1L, 2L, 3L, 1L, 2L, 3L, 1L, 2L, 3L), .Label = c("V2", "V3", "V4"), class = "factor"), value = c(0.00051, 0.00055, 0.00056, 0.00074, 0.00079, 0.00083, 0.00093, 0.00082, 0.00073, 0.0011, 0.00113, 0

How to show whiskers and points on violin plots?

由 痞子三分冷 提交于 2019-12-01 19:34:32
问题 I have a dataframe df with the following data. I want to plot the logCPM expression of the gene between two groups A and B. Samples Type GeneA Sample1 B 14.82995162 Sample2 B 12.90512275 Sample3 B 9.196524783 Sample4 A 19.42866012 Sample5 A 19.70386922 Sample6 A 16.22906914 Sample7 A 12.48966785 Sample8 B 15.53280377 Sample9 A 9.345795955 Sample10 B 9.196524783 Sample11 B 9.196524783 Sample12 B 9.196524783 Sample13 A 9.434355615 Sample14 A 15.27604692 Sample15 A 18.90867329 Sample16 B 11

How to show whiskers and points on violin plots?

由 故事扮演 提交于 2019-12-01 18:34:30
I have a dataframe df with the following data. I want to plot the logCPM expression of the gene between two groups A and B. Samples Type GeneA Sample1 B 14.82995162 Sample2 B 12.90512275 Sample3 B 9.196524783 Sample4 A 19.42866012 Sample5 A 19.70386922 Sample6 A 16.22906914 Sample7 A 12.48966785 Sample8 B 15.53280377 Sample9 A 9.345795955 Sample10 B 9.196524783 Sample11 B 9.196524783 Sample12 B 9.196524783 Sample13 A 9.434355615 Sample14 A 15.27604692 Sample15 A 18.90867329 Sample16 B 11.71503095 Sample17 B 13.7632545 Sample18 A 9.793864295 Sample19 B 9.196524783 Sample20 A 14.52562066

Use dataframe variable names in plot titles

由 左心房为你撑大大i 提交于 2019-11-29 16:47:30
I have a dataframe with several variables that I wish to label and then use in several ggplots. I have applied labels using the labeller package with the following code. library(tidyverse) library(labeller) library(ggpubr) example.df <- data.frame( origin = sample(c("hum_1", "mou_1"), 100, replace = TRUE), v1 = rnorm(100, 100, 5), v2 = rnorm(100, 10,5), v3 = rnorm (100, 25, 5)) example.df <- example.df %>% set_variable_labels(origin = "original sample", v1 = "effect of Rx", v2 = "response", v3 = "weight (kg)") This gets the labels to show up in the dataframe. However, when I use ggqqplot from

R ggplot2 boxplots - ggpubr stat_compare_means not working properly

由 两盒软妹~` 提交于 2019-11-28 11:40:52
I am trying to add significance levels to my boxplots in the form of asterisks using ggplot2 and the ggpubr package, but I have many comparisons and I only want to show the significant ones. I try to use the option hide.ns=TRUE in stat_compare_means , but it clearly does not work , it might be a bug in the ggpubr package. Besides, you see that I leave out group "PGMC4" from the pairwise wilcox.test comparisons; how can I leave this group out also for the kruskal.test ? The last question I have is how the significance level works? As in * is significant below 0.05, ** below 0.025, *** below 0
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