Skip to content

Commit

Permalink
“1.6.5”
Browse files Browse the repository at this point in the history
  • Loading branch information
Khodadadi-Jamayran committed Oct 7, 2021
1 parent 19a8254 commit 71ca678
Show file tree
Hide file tree
Showing 70 changed files with 40 additions and 561 deletions.
4 changes: 2 additions & 2 deletions DESCRIPTION
Original file line number Diff line number Diff line change
@@ -1,7 +1,7 @@
Package: iCellR
Type: Package
Title: Analyzing High-Throughput Single Cell Sequencing Data
Version: 1.6.4
Version: 1.6.5
Authors@R: c(
person(given = 'Alireza', family = 'Khodadadi-Jamayran',role = c('aut','cre'), email = '[email protected]', comment = c(ORCID = '0000-0003-2495-7504')),
person(given = 'Joseph', family = 'Pucella',role = c('aut','ctb'), comment = c(ORCID = '0000-0003-0875-8046')),
Expand All @@ -27,7 +27,7 @@ RoxygenNote: 7.1.1
BugReports: https://github.com/rezakj/iCellR/issues
URL: https://github.com/rezakj/iCellR
NeedsCompilation: yes
Packaged: 2021-06-07 15:57:39 UTC; khodaa01
Packaged: 2021-10-07 18:26:50 UTC; khodaa01
Author: Alireza Khodadadi-Jamayran [aut, cre]
(<https://orcid.org/0000-0003-2495-7504>),
Joseph Pucella [aut, ctb] (<https://orcid.org/0000-0003-0875-8046>),
Expand Down
File renamed without changes.
File renamed without changes.
File renamed without changes.
3 changes: 0 additions & 3 deletions R/F004.R → R/F0004.R
Original file line number Diff line number Diff line change
Expand Up @@ -7,9 +7,6 @@
#' @param s.phase.genes A character vector of gene names for S phase, default = s.phase.
#' @param g2m.phase.genes A character vector of gene names for G2 and M phase, default = g2m.phase.
#' @return The data frame object
#' @examples
#' New.demo.obj <- qc.stats(demo.obj)
#' head(New.demo.obj@stats)
#' @export
qc.stats <- function (x = NULL,
which.data = "raw.data",
Expand Down
10 changes: 0 additions & 10 deletions R/F005.R → R/F0005.R
Original file line number Diff line number Diff line change
Expand Up @@ -12,16 +12,6 @@
#' @param interactive If set to TRUE an interactive HTML file will be created, default = TRUE.
#' @param out.name If "interactive" is set to TRUE, the out put name for HTML, default = "plot".
#' @return An object of class iCellR.
#' @examples
#' stats.plot(demo.obj,
#' plot.type = "three.in.one",
#' out.name = "UMI-plot",
#' interactive = FALSE,
#' cell.color = "slategray3",
#' cell.size = 1,
#' cell.transparency = 0.5,
#' box.color = "red",
#' box.line.col = "green")
#' @import gridExtra
#' @importFrom htmlwidgets saveWidget
#' @importFrom plotly ggplotly layout plot_ly
Expand Down
11 changes: 0 additions & 11 deletions R/F006.R → R/F0006.R
Original file line number Diff line number Diff line change
Expand Up @@ -13,17 +13,6 @@
#' @param filter.by.gene A character vector of gene names to be filtered by thier expression. If more then one gene is defined it would be OR not AND.
#' @param filter.by.gene.exp.min Minimum gene expression to be filtered by the genes set in filter.by.gene, default = 1.
#' @return An object of class iCellR.
#' @examples
#' demo.obj <- cell.filter(demo.obj,
#' min.mito = 0,
#' max.mito = 0.05 ,
#' min.genes = 100,
#' max.genes = 2500,
#' min.umis = 0,
#' max.umis = Inf)
#'
#' message([email protected])
#'
#' @export
cell.filter <- function (x = NULL,
min.mito = 0,
Expand Down
5 changes: 0 additions & 5 deletions R/F007.R → R/F0007.R
Original file line number Diff line number Diff line change
Expand Up @@ -3,11 +3,6 @@
#' This function takes an object of class iCellR and down samples the condition to have equal number of cells in each condition.
#' @param x An object of class iCellR.
#' @return An object of class iCellR.
#' @examples
#'
#' my.obj <- down.sample(demo.obj)
#'
#'
#' @export
down.sample <- function (x = NULL) {
if ("iCellR" != class(x)[1]) {
Expand Down
4 changes: 0 additions & 4 deletions R/F008.R → R/F0008.R
Original file line number Diff line number Diff line change
Expand Up @@ -12,10 +12,6 @@
#' @param ATAC.data If TURE, it would normalize ATAC-Seq data and not RNA-Seq, default = FALSE.
#' @param ATAC.filter If TURE, all the cells filtered in RNA-Seq will be filtered in ATAC-Seq. This needs to be done for both data to match, default = TRUE.
#' @return An object of class iCellR.
#' @examples
#'
#' demo.obj <- norm.data(demo.obj, norm.method = "ranked.glsf", top.rank = 500)
#'
#' @export
norm.data <- function (x = NULL,
norm.method = "ranked.glsf",
Expand Down
5 changes: 0 additions & 5 deletions R/F009.R → R/F0009.R
Original file line number Diff line number Diff line change
Expand Up @@ -3,11 +3,6 @@
#' This function takes an object of class iCellR and scales the normalized data.
#' @param x An object of class iCellR.
#' @return An object of class iCellR.
#' @examples
#' my.obj <- data.scale(demo.obj)
#'
#' head([email protected])[1:5]
#'
#' @export
data.scale <- function (x = NULL) {
if ("iCellR" != class(x)[1]) {
Expand Down
4 changes: 0 additions & 4 deletions R/F0010.R
Original file line number Diff line number Diff line change
Expand Up @@ -5,10 +5,6 @@
#' @param which.data Choose from "raw.data" or "main.data", default = "raw.data".
#' @param each.cond If TRUE each condition will be calculated, default = FALSE.
#' @return An object of class iCellR.
#' @examples
#' demo.obj <- gene.stats(demo.obj, which.data = "main.data")
#' head([email protected])
#'
#' @export
gene.stats <- function (x = NULL,
which.data = "raw.data",
Expand Down
20 changes: 0 additions & 20 deletions R/F0011.R
Original file line number Diff line number Diff line change
Expand Up @@ -19,26 +19,6 @@
#' @param interactive If set to TRUE an interactive HTML file will be created, default = TRUE.
#' @param out.name If "interactive" is set to TRUE, the out put name for HTML, default = "plot".
#' @return An object of class iCellR.
#' @examples
#' make.gene.model(demo.obj,
#' dispersion.limit = 1.5,
#' base.mean.rank = 500,
#' no.mito.model = TRUE,
#' mark.mito = TRUE,
#' interactive = FALSE,
#' my.out.put = "plot",
#' out.name = "gene.model")
#'
#' demo.obj <- make.gene.model(demo.obj,
#' dispersion.limit = 1.5,
#' base.mean.rank = 500,
#' no.mito.model = TRUE,
#' mark.mito = TRUE,
#' interactive = FALSE,
#' out.name = "gene.model")
#'
#' head([email protected])
#'
#' @import ggrepel
#' @export
make.gene.model <- function (x = NULL,
Expand Down
5 changes: 0 additions & 5 deletions R/F0012.R
Original file line number Diff line number Diff line change
Expand Up @@ -9,11 +9,6 @@
#' @param gene.list A charactor vector of genes to be used for PCA. If "clust.method" is set to "gene.model", default = "my_model_genes.txt".
#' @param scale.data If TRUE the data will be scaled (log2 + plus.log.value), default = TRUE.
#' @return An object of class iCellR.
#' @examples
#' demo.obj <- run.pca(demo.obj, method = "gene.model", gene.list = [email protected])
#'
#' head([email protected])[1:5]
#'
#' @export
run.pca <- function (x = NULL,
data.type = "main",
Expand Down
3 changes: 0 additions & 3 deletions R/F0013.R
Original file line number Diff line number Diff line change
Expand Up @@ -4,9 +4,6 @@
#' @param x An object of class iCellR.
#' @param pcs.in.plot Number of PCs to show in plot, defult = 50.
#' @return An object of class iCellR.
#' @examples
#' opt.pcs.plot(demo.obj)
#'
#' @export
opt.pcs.plot <- function (x = NULL, pcs.in.plot = 50) {
if ("iCellR" != class(x)[1]) {
Expand Down
6 changes: 0 additions & 6 deletions R/F0014.R
Original file line number Diff line number Diff line change
Expand Up @@ -6,12 +6,6 @@
#' @param top.pos Number of top positive marker genes to be taken from each PC, default = 15.
#' @param top.neg Number of top negative marker genes to be taken from each PC, default = 5.
#' @return An object of class iCellR.
#' @examples
#'
#' demo.obj <- find.dim.genes(demo.obj, dims = 1:10,top.pos = 20, top.neg = 20)
#'
#' head([email protected])
#'
#' @export
find.dim.genes <- function (x = NULL,
dims = 1:10,
Expand Down
11 changes: 0 additions & 11 deletions R/F0015.R
Original file line number Diff line number Diff line change
Expand Up @@ -9,17 +9,6 @@
#' @param min.clust minimum number of clusters, default = 2.
#' @param dims PCA dimentions to be use for clustering, default = 1:10.
#' @return An object of class iCellR.
#' @examples
#' demo.obj <- run.clustering(demo.obj,
#' clust.method = "kmeans",
#' dist.method = "euclidean",
#' index.method = "silhouette",
#' max.clust = 2,
#' min.clust = 2,
#' dims = 1:10)
#'
#' head([email protected])
#'
#' @import NbClust
#' @export
run.clustering <- function (x = NULL,
Expand Down
5 changes: 0 additions & 5 deletions R/F0017.R
Original file line number Diff line number Diff line change
Expand Up @@ -23,11 +23,6 @@
#' @param eta numeric; Learning rate (default: 200.0)
#' @param exaggeration_factor numeric; Exaggeration factor used to multiply the P matrix in the first part of the optimization (default: 12.0)
#' @return An object of class iCellR.
#' @examples
#' demo.obj <- run.pc.tsne(demo.obj, dims = 1:10,perplexity = 20)
#'
#' head([email protected])[1:5]
#'
#' @import Rtsne
#' @export
run.pc.tsne <- function (x = NULL,
Expand Down
4 changes: 0 additions & 4 deletions R/F0018.R
Original file line number Diff line number Diff line change
Expand Up @@ -286,10 +286,6 @@
#' @param verbose If \code{TRUE}, log details to the console.
#'
#' @return An object of class iCellR.
#' @examples
#' demo.obj <- run.umap(demo.obj, dims = 1:10)
#' head([email protected])
#'
#' @import uwot
#' @export
run.umap <- function (x = NULL,
Expand Down
12 changes: 0 additions & 12 deletions R/F0020.R
Original file line number Diff line number Diff line change
Expand Up @@ -20,18 +20,6 @@
#' @param density If TRUE the density plots for PCA/tSNE second dimension will be created, default = FALSE.
#' @param static3D If TRUE a non-interactive 3D plot will be made.
#' @return An object of class iCellR.
#' @examples
#' cluster.plot(demo.obj,plot.type = "umap",interactive = FALSE)
#'
#' cluster.plot(demo.obj,plot.type = "tsne",interactive = FALSE)
#'
#' cluster.plot(demo.obj,plot.type = "pca",interactive = FALSE)
#'
#' cluster.plot(demo.obj,plot.type = "pca",col.by = "conditions",interactive = FALSE)
#'
#' cluster.plot(demo.obj,plot.type = "umap",col.by = "conditions",interactive = FALSE)
#'
#' cluster.plot(demo.obj,plot.type = "tsne",col.by = "conditions",interactive = FALSE)
#' @import RColorBrewer
#' @import scatterplot3d
#' @importFrom htmlwidgets saveWidget
Expand Down
9 changes: 0 additions & 9 deletions R/F0025.R
Original file line number Diff line number Diff line change
Expand Up @@ -6,15 +6,6 @@
#' @param to.clust The new name for the cluster.
#' @param clust.reset Reset to the original clustering.
#' @return An object of class iCellR.
#' @examples
#' demo.obj <- change.clust(demo.obj, change.clust = 1, to.clust = 3)
#' cluster.plot(demo.obj,plot.type = "umap",interactive = FALSE)
#'
#' demo.obj <- change.clust(demo.obj, change.clust = 3, to.clust = "B Cell")
#' cluster.plot(demo.obj,plot.type = "umap",interactive = FALSE)
#'
#' demo.obj <- change.clust(demo.obj, clust.reset = TRUE)
#' cluster.plot(demo.obj,plot.type = "umap",interactive = FALSE)
#' @export
change.clust <- function (x = NULL,
change.clust = 0,
Expand Down
5 changes: 0 additions & 5 deletions R/F0027.R
Original file line number Diff line number Diff line change
Expand Up @@ -14,11 +14,6 @@
#' @param out.name If "interactive" is set to TRUE, the out put name for HTML, default = "plot".
#' @param conds.to.plot Choose the conditions you want to see in the plot, default = NULL (all conditions).
#' @return An object of class iCellR.
#' @examples
#' clust.stats.plot(demo.obj,
#' plot.type = "box.mito",
#' interactive = FALSE,
#' out.name = "box.mito.clusters")
#' @export
clust.stats.plot <- function (x = NULL,
plot.type = "box.mito",
Expand Down
3 changes: 0 additions & 3 deletions R/F0029.R
Original file line number Diff line number Diff line change
Expand Up @@ -7,9 +7,6 @@
#' @param filt.ambig Filter markers that are seen for more than one cluster, default = TRUE.
#' @param cluster Choose a cluster to find markers for. If 0, it would find markers for all clusters, , default = 0.
#' @return A set of gene names
#' @examples
#' marker.genes <- findMarkers(demo.obj,fold.change = 2,padjval = 0.1,uniq = TRUE)
#' top.markers(marker.genes, topde = 10, min.base.mean = 0.8)
#' @import Matrix
#' @export
top.markers <- function (x = NULL, topde = 10,
Expand Down
10 changes: 0 additions & 10 deletions R/F0030.R
Original file line number Diff line number Diff line change
Expand Up @@ -16,16 +16,6 @@
#' @param cex.col Chhose a size, default = 10.
#' @param cex.row Choose a size, default = 10.
#' @return An object of class iCellR
#' @examples
#' marker.genes <- findMarkers(demo.obj,fold.change = 2,padjval = 0.1,uniq = TRUE)
#'
#' MyGenes <- top.markers(marker.genes, topde = 10, min.base.mean = 0.8)
#'
#' heatmap.gg.plot(demo.obj,
#' gene = MyGenes,
#' out.name = "plot",
#' cluster.by = "clusters",
#' interactive = FALSE)
#' @import pheatmap
#' @importFrom reshape melt
#' @importFrom htmlwidgets saveWidget
Expand Down
15 changes: 0 additions & 15 deletions R/F0031.R
Original file line number Diff line number Diff line change
Expand Up @@ -27,21 +27,6 @@
#' @param out.name If "interactive" is set to TRUE, the out put name for HTML, default = "plot".
#' @param write.data Write export the data used for the plot plot, default = TFALSE.
#' @return An object of class iCellR.
#' @examples
#' gene.plot(demo.obj, gene = "CD74",interactive = FALSE)
#'
#' gene.plot(demo.obj, gene = "CD74",plot.data.type = "umap",interactive = FALSE)
#'
#' gene.plot(demo.obj, gene = "CD74",
#' plot.data.type = "umap",
#' interactive = FALSE,
#' plot.type = "barplot")
#'
#' gene.plot(demo.obj, gene = "CD74",
#' plot.data.type = "umap",
#' interactive = FALSE,
#' plot.type = "boxplot")
#'
#' @importFrom ggpubr stat_compare_means
#' @import plyr
#' @importFrom htmlwidgets saveWidget
Expand Down
10 changes: 0 additions & 10 deletions R/F0032.R
Original file line number Diff line number Diff line change
Expand Up @@ -11,16 +11,6 @@
#' @param type Choose from "classic", "jitter", "unrooted", "fan", "cladogram", "radial", default = "classic".
#' @param cex Text size, default = 1.
#' @return An object of class iCellR.
#' @examples
#' marker.genes <- findMarkers(demo.obj,fold.change = 2,padjval = 0.1,uniq = TRUE)
#'
#' MyGenes <- top.markers(marker.genes, topde = 10, min.base.mean = 0.8)
#'
#' pseudotime.tree(demo.obj,
#' marker.genes = MyGenes,
#' type = "unrooted",
#' clust.method = "complete")
#'
#' @import gridExtra
#' @import ggdendro
#' @import ape
Expand Down
5 changes: 0 additions & 5 deletions R/F0034.R
Original file line number Diff line number Diff line change
Expand Up @@ -10,11 +10,6 @@
#' @param pval.test Choose from "t.test", "wilcox.test", default = "t.test".
#' @param p.adjust.method Correction method. Choose from "holm", "hochberg", "hommel", "bonferroni", "BH", "BY","fdr", "none", default = "hochberg".
#' @return An object of class iCellR
#' @examples
#' diff.res <- run.diff.exp(demo.obj, de.by = "clusters", cond.1 = c(1), cond.2 = c(2))
#'
#' head(diff.res)
#'
#' @export
run.diff.exp <- function (x = NULL,
data.type = "main",
Expand Down
16 changes: 0 additions & 16 deletions R/F0035.R
Original file line number Diff line number Diff line change
Expand Up @@ -15,22 +15,6 @@
#' @param interactive If set to TRUE an interactive HTML file will be created, default = TRUE.
#' @param out.name If "interactive" is set to TRUE, the output name for HTML, default = "plot".
#' @return Plots
#' @examples
#'
#' diff.res <- run.diff.exp(demo.obj, de.by = "clusters", cond.1 = c(1), cond.2 = c(2))
#'
#' volcano.ma.plot(diff.res,
#' sig.value = "pval",
#' sig.line = 0.05,
#' plot.type = "volcano",
#' interactive = FALSE)
#'
#' volcano.ma.plot(diff.res,
#' sig.value = "pval",
#' sig.line = 0.05,
#' plot.type = "ma",
#' interactive = FALSE)
#'
#' @importFrom grDevices col2rgb colorRampPalette rgb
#' @importFrom methods new
#' @importFrom stats aggregate as.dendrogram cor cor.test dist hclust p.adjust prcomp quantile sd t.test
Expand Down
11 changes: 0 additions & 11 deletions R/F0039.R
Original file line number Diff line number Diff line change
Expand Up @@ -4,17 +4,6 @@
#' @param vdj.data A data frame containing vdj information.
#' @param cond.name Conditions.
#' @return An object of class iCellR
#' @examples
#' my.vdj <- read.csv(file = system.file('extdata', 'all_contig_annotations.csv',
#' package = 'iCellR'),
#' as.is = TRUE)
#' head(my.vdj)
#' dim(my.vdj)
#'
#' My.VDJ <- prep.vdj(vdj.data = my.vdj, cond.name = "NULL")
#' head(My.VDJ)
#' dim(My.VDJ)
#'
#' @export
prep.vdj <- function (vdj.data = "data.frame", cond.name = "NULL") {
# read VDJ data
Expand Down
13 changes: 0 additions & 13 deletions R/F0040.R
Original file line number Diff line number Diff line change
Expand Up @@ -4,19 +4,6 @@
#' @param x An object of class iCellR.
#' @param vdj.data A data frame containing VDJ information for cells.
#' @return An object of class iCellR
#' @examples
#' my.vdj <- read.csv(file = system.file('extdata', 'all_contig_annotations.csv',
#' package = 'iCellR'),
#' as.is = TRUE)
#' head(my.vdj)
#' dim(my.vdj)
#'
#' My.VDJ <- prep.vdj(vdj.data = my.vdj, cond.name = "NULL")
#' head(My.VDJ)
#' dim(My.VDJ)
#'
#' my.obj <- add.vdj(demo.obj, vdj.data = My.VDJ)
#'
#' @export
add.vdj <- function (x = NULL, vdj.data = "data.frame") {
if ("iCellR" != class(x)[1]) {
Expand Down
Loading

0 comments on commit 71ca678

Please sign in to comment.