I am trying to generate a bar plot with this data:
library(sjPlot)
library(sjstats)
data("efc")
i use the following to generate the default xtab plot from the sjPlot.
sjp.xtab(x = efc$e42dep,
grp = efc$c82cop1)
But i prefer show only a "cleanest" plot, without information (i prefer to link to a table if you want the specific data), so i try this:
sjp.xtab(x = efc$e42dep,
grp = efc$c82cop1,show.total = F, show.n = F,show.prc = F)
but i get this
Error in sjp.xtab(x = efc$e42dep, grp = efc$c82cop1, show.total = F,
show.n = F, : objeto 'ggvaluelabels' no encontrado
i use R in a Spanish language OS, so...
is basically
object 'ggvaluelabels' not found
What am i doing wrong?
use show.values = FALSE to prevent annotating the graph.
sjp.xtab(x = efc$e42dep, grp = efc$c82cop1)
# show.values = FALSE
sjp.xtab(x = efc$e42dep, grp = efc$c82cop1, show.values = FALSE )
sjp.xtab(x = efc$e42dep, grp = efc$c82cop1,show.total = F, show.n = F,show.prc = F, show.values = FALSE)
Related
Hello I'm a new bioinformatician so bear with me please!
I'm using the gprofiler2 to run GO/KEGG analysis in R using emacs/ess and I want to add a title to the table it offers:
publish_gosttable(gostres, highlight_terms = gostres$result[c(1:2,10,120),],
use_colors = TRUE,
show_columns = c("source", "term_name", "term_size", "intersection_size"),
filename = NULL)
I have tried the title(), tab_header() function but I can't seem to be able to add a title. My question is if there is some other function or package that would allow me to add it instead of having to do it manually.
The code so far
GOresult <- gost(
geneid1up$gene,
organism = "hsapiens",
ordered_query = FALSE,
multi_query = FALSE,
significant = TRUE,
exclude_iea = FALSE,
measure_underrepresentation = FALSE,
evcodes = FALSE,
user_threshold = 0.05,
correction_method = "gSCS",
domain_scope = "annotated",
custom_bg = NULL,
numeric_ns = "",
sources = c("GO:BP","GO:MF","GO:CC","KEGG"),
as_short_link = FALSE)
GOresult1 <- as.data.frame(GOresult$result)
GOresult1$minuslog10pval <- -log10(GOresult1$p_value)
names(GOresult1)[15] <- "-log10(pval)"
GOresult2 <- GOresult1[order(GOresult1$p_value, decreasing=F),]
plot1 <- publish_gosttable(GOresult2, highlight_terms = GOresult2[c(1:20),],
use_colors = FALSE,
show_columns = c("source", "term_name", "term_size", "intersection_size","-log10(pval)"),
filename = NULL)
Does this do the job?
library(gprofiler2)
library(ggplot2)
gostres <- gost(query = c("X:1000:1000000", "rs17396340", "GO:0005005", "ENSG00000156103", "NLRP1"),
organism = "hsapiens", ordered_query = FALSE,
multi_query = FALSE, significant = TRUE, exclude_iea = FALSE,
measure_underrepresentation = FALSE, evcodes = FALSE,
user_threshold = 0.05, correction_method = "g_SCS",
domain_scope = "annotated", custom_bg = NULL,
numeric_ns = "", sources = NULL, as_short_link = FALSE)
publish_gosttable(gostres, highlight_terms = gostres$result[c(1:2,10,120),],
use_colors = TRUE,
show_columns = c("source", "term_name", "term_size", "intersection_size"),
filename = NULL)+
ggtitle('Your Title')
Result:
The trick is that the plot is a ggplot objet. Therefore you can add the title using +ggtitle('Your Title') after your plot code (as in my example)
I am trying to run the Monocle3 function find_gene_modules() on a cell_data_set (cds) but am getting a variety of errors in this. I have not had any other issues before this. I am working with an imported Seurat object. My first error came back stating that the number of rows were not the same between my cds and cds#preprocess_aux$gene_loadings values. I took a look and it seems my gene loadings were a list under cds#preprocess_aux#listData$gene_loadings. I then ran the following code to make a dataframe version of the gene loadings:
test <- seurat#assays$RNA#counts#Dimnames[[1]]
test <- as.data.frame(test)
cds#preprocess_aux$gene_loadings <- test
rownames(cds#preprocess_aux$gene_loadings) <- cds#preprocess_aux$gene_loadings[,1]
Which created a cds#preprocess_aux$gene_loadings dataframe with the same number of rows and row names as my cds. This resolved my original error but now led to a new error being thrown from uwot as:
15:34:02 UMAP embedding parameters a = 1.577 b = 0.8951
Error in uwot(X = X, n_neighbors = n_neighbors, n_components = n_components, :
No numeric columns found
Running traceback() produces the following information.
> traceback()
4: stop("No numeric columns found")
3: uwot(X = X, n_neighbors = n_neighbors, n_components = n_components,
metric = metric, n_epochs = n_epochs, alpha = learning_rate,
scale = scale, init = init, init_sdev = init_sdev, spread = spread,
min_dist = min_dist, set_op_mix_ratio = set_op_mix_ratio,
local_connectivity = local_connectivity, bandwidth = bandwidth,
gamma = repulsion_strength, negative_sample_rate = negative_sample_rate,
a = a, b = b, nn_method = nn_method, n_trees = n_trees, search_k = search_k,
method = "umap", approx_pow = approx_pow, n_threads = n_threads,
n_sgd_threads = n_sgd_threads, grain_size = grain_size, y = y,
target_n_neighbors = target_n_neighbors, target_weight = target_weight,
target_metric = target_metric, pca = pca, pca_center = pca_center,
pca_method = pca_method, pcg_rand = pcg_rand, fast_sgd = fast_sgd,
ret_model = ret_model || "model" %in% ret_extra, ret_nn = ret_nn ||
"nn" %in% ret_extra, ret_fgraph = "fgraph" %in% ret_extra,
batch = batch, opt_args = opt_args, epoch_callback = epoch_callback,
tmpdir = tempdir(), verbose = verbose)
2: uwot::umap(as.matrix(preprocess_mat), n_components = max_components,
metric = umap.metric, min_dist = umap.min_dist, n_neighbors = umap.n_neighbors,
fast_sgd = umap.fast_sgd, n_threads = cores, verbose = verbose,
nn_method = umap.nn_method, ...)
1: find_gene_modules(cds[pr_deg_ids, ], reduction_method = "UMAP",
max_components = 2, umap.metric = "cosine", umap.min_dist = 0.1,
umap.n_neighbors = 15L, umap.fast_sgd = FALSE, umap.nn_method = "annoy",
k = 20, leiden_iter = 1, partition_qval = 0.05, weight = FALSE,
resolution = 0.001, random_seed = 0L, cores = 1, verbose = T)
I really have no idea what I am doing wrong or how to proceed from here. Does anyone with experience with uwot know where my error is coming from? Really appreciate the help!
I'm using Heatmap from the package complexheatmap
in the script, I need to create a variable ha_column that I will incorporate into my script.
ha_column = HeatmapAnnotation (df = data.frame(type1=c(rep("name1",5), rep("name2",5),rep("name3",5), col = list(type1=c("name1" = "#DCDCDC", "name2" = "#DC928B", "name2"="#BA72D3")))))
I have 2 vectors:
vectors1=c("name1","name2","name3)
vectors2=c("#DCDCDC","#DC928B","#BA72D3")
and the idea is to reproduce the above script with these two vectors.
I tried:
paste0("ha_column = HeatmapAnnotation(df = data.frame(type1 = c(rep(",vectors1,", 5),col = list(type1 = c(",vectors1,"=",vectors2,")))")
bu it only paste line by line such as:
[1] "ha_column = HeatmapAnnotation(df = data.frame(type1 = c(rep(name1, 5),col = list(type1 = c(name1=#DCDCDC)))"
[2] "ha_column = HeatmapAnnotation(df = data.frame(type1 = c(rep(name2, 5),col = list(type1 = c(name2=#DC928B)))"
[3] "ha_column = HeatmapAnnotation(df = data.frame(type1 = c(rep(name3, 5),col = list(type1 = c(name3=#BA72D3)))"
instead of doing what I want ...
Does anyone have an idea?
Thanks for your time.
It's generally not a good idea to build code as a string. Instead think of building a function to do what you want.
You could do something line
ha_column_fun = function(names, colors) {
HeatmapAnnotation(
df = data.frame(type1 = rep(names, each=5)),
col = list(type1=setNames(colors, names))
)
}
And then you could call it with
ha_column = ha_column_fun(vectors1, vectors2)
I used the bibliometrix function in R, and want to plot some useful graphs.
library(bibliometrix)
??bibliometrix
D<-readFiles("E:\\RE\\savedrecs.txt")
M <- convert2df(D,dbsource = "isi", format= "plaintext")
results <- biblioAnalysis(M ,sep = ";" )
S<- summary(object=results,k=10, pause=FALSE)
plot(x=results,k=10,pause=FALSE)
options(width=100)
S <- summary(object = results, k = 10, pause = FALSE)
NetMatrix <- biblioNetwork(M1, analysis = "co-occurrences", network = "author_keywords", sep = ";")
S <- normalizeSimilarity(NetMatrix, type = "association")
net <- networkPlot(S, n = 200, Title = "co-occurrence network",type="fruchterman", labelsize = 0.7, halo = FALSE, cluster = "walktrap",remove.isolates=FALSE, remove.multiple=FALSE, noloops=TRUE, weighted=TRUE)
res <- thematicMap(net, NetMatrix, S)
plot(res$map)
But in the net <- networkPlot(S, n = 200, Title = "co-occurrence network",type="fruchterman", labelsize = 0.7, halo = FALSE, cluster = "walktrap",remove.isolates=FALSE, remove.multiple=FALSE, noloops=TRUE, weighted=TRUE), it shows error
Error in V<-(*tmp*, value = *vtmp*) : invalid indexing
. Also I cannot do the CR, it always shows unlistCR. I cannot use the NetMatrix function neither.
Some help me plsssssssss
The problem is in the data itself not in the code you presented. When I downloaded the data from bibliometrix.com and changed M1 to M (typo?) in biblioNetwork function call everything worked perfectly. Please see the code below:
library(bibliometrix)
# Plot bibliometric analysis results
D <- readFiles("http://www.bibliometrix.org/datasets/savedrecs.txt")
M <- convert2df(D, dbsource = "isi", format= "plaintext")
results <- biblioAnalysis(M, sep = ";")
S <- summary(results)
plot(x = results, k = 10, pause = FALSE)
# Plot Bibliographic Network
options(width = 100)
S <- summary(object = results, k = 10, pause = FALSE)
NetMatrix <- biblioNetwork(M, analysis = "co-occurrences", network = "author_keywords", sep = ";")
S <- normalizeSimilarity(NetMatrix, type = "association")
net <- networkPlot(S, n = 200, Title = "co-occurrence network", type = "fruchterman",
labelsize = 0.7, halo = FALSE, cluster = "walktrap",
remove.isolates = FALSE, remove.multiple = FALSE, noloops = TRUE, weighted = TRUE)
# Plot Thematic Map
res <- thematicMap(net, NetMatrix, S)
str(M)
plot(res$map)
I'm trying to create a phylogeny where the branch lengths that I've coded are represented by colour rather than length. So I want the branch lengths to be equal.
Here is my code:
plotBranchbyTrait(tree.scaled, tree.scaled$edge.length, mode=c("edges"),palette="rainbow", use.edge.length = FALSE, node.depth = 2)
It's my understanding that use.edge.length = FALSE should make the branch lengths equal, and it does this if I code the tree using plot.phylo(). But the tree still shows up with the branch lengths when I use plotBranchbyTrait(). Anyone know how to get around this?
Unfortunately, optional arguments (...) are not directly passed to plot.phylo in the plotBranchbyTrait function. One non-elegant way to fix that is to modify the body directly in R to add a hard coded use.edge.length = FALSE option.
You can do this by creating a new function and modify it using body(foo)[[line_of_interest]] <- substitute(my_new_line <- that_does_something). The following example should work:
## Back up the function
plotBranchbyTrait_no_edge_length <- phytools::plotBranchbyTrait
## The line to modify:
body(plotBranchbyTrait_no_edge_length)[[34]]
# xx <- plot.phylo(tree, type = type, show.tip.label = show.tip.label,
# show.node.label = show.node.label, edge.color = colors, edge.width = edge.width,
# edge.lty = edge.lty, font = font, cex = cex, adj = adj, srt = srt,
# no.margin = no.margin, root.edge = root.edge, label.offset = label.offset,
# underscore = underscore, x.lim = x.lim, y.lim = y.lim, direction = direction,
# lab4ut = lab4ut, tip.color = tip.color, plot = plot, rotate.tree = rotate.tree,
# open.angle = open.angle, lend = 2, new = FALSE)
## Modify the line 34 by adding `use.edge.length = FALSE`
body(plotBranchbyTrait_no_edge_length)[[34]] <- substitute( xx <- plot.phylo(use.edge.length = FALSE, tree, type = type, show.tip.label = show.tip.label, show.node.label = show.node.label, edge.color = colors, edge.width = edge.width, edge.lty = edge.lty, font = font, cex = cex, adj = adj, srt = srt, no.margin = no.margin, root.edge = root.edge, label.offset = label.offset, underscore = underscore, x.lim = x.lim, y.lim = y.lim, direction = direction, lab4ut = lab4ut, tip.color = tip.color, plot = plot, rotate.tree = rotate.tree, open.angle = open.angle, lend = 2, new = FALSE) )
## Testing whether it worked
library(phytools)
tree <- pbtree(n=50)
x <- fastBM(tree)
## With use.edge.length = TRUE (default)
plotBranchbyTrait(tree, x, mode = "tips", edge.width = 4, prompt = FALSE)
## With use.edge.length = FALSE
plotBranchbyTrait_no_edge_length(tree, x, mode = "tips", edge.width = 4, prompt = FALSE)
You can find more on how to modify functions here.