chore: update docs

Author: pacmandoh

DESCRIPTION

@@ -8,7 +8,7 @@ Description: Some useful functions to visualize scRNA-seq figures.
 License: MIT + file LICENSE
 Encoding: UTF-8
 Roxygen: list(markdown = TRUE)
-RoxygenNote: 7.2.3
+RoxygenNote: 7.3.1
 Remotes:
  junjunlab/jjAnno,
  junjunlab/jjPlot,

NAMESPACE

@@ -1,15 +1,15 @@
 # Generated by roxygen2: do not edit by hand
 
 export("%>%")
-export(AverageHeatmap)
-export(FeatureCornerAxes)
+export(averageHeatmap)
 export(cellRatioPlot)
 export(clusterCornerAxes)
 export(drawLegend)
+export(featureCornerAxes)
 export(featurePlot)
 export(jjDotPlot)
 export(jjVolcano)
-export(markerVocalno)
+export(markerVolcano)
 export(scatterCellPlot)
 export(tracksPlot)
 import(Seurat)

R/averageHeatmap.R

@@ -1,6 +1,7 @@
-#' @name AverageHeatmap
+#' @name averageHeatmap
 #' @author Junjun Lao
 #' @title Plot averaged gene expression cross cluster cells
+#'
 #' @param object object seurat object.
 #' @param markerGene Your marker genes.
 #' @param group.by Categories for grouping (e.g, ident, replicate, celltype). "ident" by default.
@@ -42,13 +43,13 @@
 #' markers <- read.table(markergene, sep = ",", header = TRUE)
 #'
 #' # plot
-#' AverageHeatmap(
+#' averageHeatmap(
 #' object = pbmc,
 #' markerGene = markers$gene
 #' )
 #'
 #' # change color
-#' AverageHeatmap(
+#' averageHeatmap(
 #' object = pbmc,
 #' markerGene = markers$gene,
 #' htCol = c("#339933", "#FFCC00", "#FF0033")

R/clusterCornerAxes.R

@@ -1,6 +1,7 @@
 #' @name clusterCornerAxes
 #' @author Junjun Lao
 #' @title Add corner axes on seurat UMAP/tSNE cluster figures
+#'
 #' @param object seurat object.
 #' @param reduction "string", reduction type (umap/tsne).
 #' @param groupFacet "string", give the column name in seurat metadata to facet plot.

R/featureCornerAxes.R

@@ -1,6 +1,7 @@
-#' @name FeatureCornerAxes
+#' @name featureCornerAxes
 #' @author Junjun Lao
 #' @title Add corner axes on seurat UMAP/tSNE gene FeaturePlot function figures
+#'
 #' @param object object seurat object.
 #' @param reduction "string", reduction type (umap/tsne).
 #' @param features "string", the gene you want to plot.
@@ -33,15 +34,15 @@
 #' tmp <- readRDS(test)
 #'
 #' # umap
-#' FeatureCornerAxes(
+#' featureCornerAxes(
 #' object = tmp, reduction = "umap",
 #' groupFacet = "orig.ident",
 #' relLength = 0.5, relDist = 0.2,
 #' features = c("Actb", "Ythdc1", "Ythdf2")
 #' )
 #'
 #' # one axes
-#' FeatureCornerAxes(
+#' featureCornerAxes(
 #' object = tmp, reduction = "umap",
 #' groupFacet = "orig.ident",
 #' features = c("Actb", "Ythdc1", "Ythdf2"),
@@ -51,7 +52,7 @@
 #' )
 #'
 #' # tsne
-#' FeatureCornerAxes(
+#' featureCornerAxes(
 #' object = tmp, reduction = "tsne",
 #' groupFacet = "orig.ident",
 #' relLength = 0.5, relDist = 0.2,

R/featurePlot.R

@@ -1,9 +1,7 @@
-#' featurePlot Function
-#'
-#' This function creates a scatter plot for multiple genes or features from a
-#' Seurat object.
-#'
+#' @name featurePlot
 #' @author Jun Zhang
+#' @title This function creates a scatter plot for multiple genes or features from a
+#' Seurat object.
 #'
 #' @param object A Seurat object containing the data.
 #' @param dim The dimension to use for plotting, default is "umap".

R/markerVolcano.R

@@ -1,6 +1,7 @@
 #' @name markerVolcano
 #' @author Junjun Lao
 #' @title Marker genes volcano plot
+#'
 #' @param markers Dataframe marker genes from findAllmarkers function from seurat.
 #' @param ownGene Your own gene names to be labeled on plot, defaults is null.
 #' @param topn Numbers top genes to label, defaults is 5.

R/scatterCellPlot.R

@@ -1,8 +1,6 @@
-#' Scatter Cell Plot
-#'
-#' This function creates a scatter cell plot using the grid package in R.
-#'
+#' @name scatterCellPlot
 #' @author Jun Zhang
+#' @title This function creates a scatter cell plot using the grid package in R.
 #'
 #' @param object A Seurat object containing the data.
 #' @param color A vector of colors for each cell type. If NULL, random colors will be assigned.

R/tracksPlot.R

@@ -1,8 +1,6 @@
-#' Generate a track or heatmap plot
-#'
-#' This function generates a track or heatmap plot based on the provided data.
-#'
+#' @name tracksPlot
 #' @author Jun Zhang
+#' @title This function generates a track or heatmap plot based on the provided data.
 #'
 #' @param object An optional object containing the data.
 #' @param plot.type The type of plot to generate, either "track" or "heatmap".

README.md

@@ -1,7 +1,8 @@
 # scRNAtoolVis <img src="man/scRNAtoolVis-logo.png" align="right" height="200" />
+
  Some useful function to make your scRNA-seq plot more beautiful.
- 
- ## Installation
+
+## Installation
 
 ```R
 install.packages('devtools')
@@ -15,10 +16,11 @@ library(scRNAtoolVis)
 
 ## Citation
 
-> Jun Zhang (2022). *scRNAtoolVis: Useful Functions to Make Your scRNA-seq Plot More Cool!.* https://github.com/junjunlab/scRNAtoolVis, https://junjunlab.github.io/scRNAtoolVis-manual/.
+> Jun Zhang (2022). *scRNAtoolVis: Useful Functions to Make Your scRNA-seq Plot More Cool!.* <https://github.com/junjunlab/scRNAtoolVis>, <https://junjunlab.github.io/scRNAtoolVis-manual/>.
 
 ## More examples see
-> - https://junjunlab.github.io/scRNAtoolVis-manual/
+>
+> - <https://junjunlab.github.io/scRNAtoolVis-manual/>
 
 ![image](https://user-images.githubusercontent.com/64965509/198531385-00b0587d-e202-4417-b11d-53cd419594e6.png)
 
@@ -29,10 +31,10 @@ library(scRNAtoolVis)
 > - [**scRNAtoolVis 0.0.3 版本更新**](https://mp.weixin.qq.com/s?__biz=MzkyMTI1MTYxNA==&mid=2247501432&idx=1&sn=93a7bb3506c911845ef7d10a2fcfdea3&chksm=c184fc09f6f3751f0c2b94f0a6d69692efcc916a45a5409f93b23f90f8db809ca750f87ba234&token=1253522169&lang=zh_CN#rd)
 > - [**jjDotPlot 优雅的可视化单细胞基因表达**](https://mp.weixin.qq.com/s?__biz=MzkyMTI1MTYxNA==&mid=2247505159&idx=1&sn=e81b7f890e93419be154b1cf432ae84f&chksm=c184ef76f6f366608d6b2b2d214aecaa4d6c57e976f9fe43a93201a3f6795051395ffc2addf4&token=1253522169&lang=zh_CN#rd)
 > - [**jjDotPlot 对基因和亚群排序**](https://mp.weixin.qq.com/s?__biz=MzkyMTI1MTYxNA==&mid=2247505344&idx=1&sn=40b5934ca798e6518172b6c5743c9d95&chksm=c184efb1f6f366a7db3d924f54e9e763c78366021a6d263a502f4d4f4a806250743a74283d5f&token=1253522169&lang=zh_CN#rd)
-> - [**AverageHeatmap 调整细胞亚群顺序**](https://mp.weixin.qq.com/s?__biz=MzkyMTI1MTYxNA==&mid=2247505603&idx=1&sn=3f85e23cc0eaffa5d92fb4aa03ca0d14&chksm=c184ecb2f6f365a41a428f5600fa9797263bb4432d51be7dc452f213bc1c9be70d50ab669159&token=1253522169&lang=zh_CN#rd)
+> - [**averageHeatmap 调整细胞亚群顺序**](https://mp.weixin.qq.com/s?__biz=MzkyMTI1MTYxNA==&mid=2247505603&idx=1&sn=3f85e23cc0eaffa5d92fb4aa03ca0d14&chksm=c184ecb2f6f365a41a428f5600fa9797263bb4432d51be7dc452f213bc1c9be70d50ab669159&token=1253522169&lang=zh_CN#rd)
 > - [**jjVolcano 一行代码绘制单细胞火山图**](https://mp.weixin.qq.com/s?__biz=MzkyMTI1MTYxNA==&mid=2247506316&idx=1&sn=307fffe550e25987b148f843e169cbcd&chksm=c184e3fdf6f36aebbe7e948d029f831f03c2906e02a271ee85900a2faac262d2c80bd1b7d2b5&token=1253522169&lang=zh_CN#rd)
 > - [**单细胞火山图的旋转和环形**](https://mp.weixin.qq.com/s?__biz=MzkyMTI1MTYxNA==&mid=2247506337&idx=1&sn=5d84b4cbddf053456561d806f3d04737&chksm=c184e3d0f6f36ac65a1cee3d353de3715c30460af0acfbc35446eac61b5b5e9170d7fb1e6315&token=1253522169&lang=zh_CN#rd)
-> - [**AverageHeatmap 对单细胞 marker 基因聚类**](https://mp.weixin.qq.com/s?__biz=MzkyMTI1MTYxNA==&mid=2247506807&idx=1&sn=f649c782a8d21765f185f03dec0fd9c5&chksm=c184e106f6f3681003142cbb48c5bc406da8458e0153bd00e805ae8fb9c01c6b25c6ff4d6156&token=1253522169&lang=zh_CN#rd)
+> - [**averageHeatmap 对单细胞 marker 基因聚类**](https://mp.weixin.qq.com/s?__biz=MzkyMTI1MTYxNA==&mid=2247506807&idx=1&sn=f649c782a8d21765f185f03dec0fd9c5&chksm=c184e106f6f3681003142cbb48c5bc406da8458e0153bd00e805ae8fb9c01c6b25c6ff4d6156&token=1253522169&lang=zh_CN#rd)
 > - [**听说你想绘制 scanpy 的 tracksPlot?**](https://mp.weixin.qq.com/s?__biz=MzkyMTI1MTYxNA==&mid=2247509478&idx=1&sn=71977a66e74d9dc4fa6aa1b2adbc50be&chksm=c1849f97f6f31681543b475f4df381c9e462dfd617260d5fbeb8956731033c97eb4c20a49f9b&token=143921488&lang=zh_CN#rd)
 > - [**用 grid 手搓一个单细胞散点图+细胞数量条形图**](https://mp.weixin.qq.com/s?__biz=MzkyMTI1MTYxNA==&mid=2247509735&idx=1&sn=212e45f9e6c8cfd13bc943b6ac806dc2&chksm=c1849c96f6f31580624e0d4bab65b47d7b3e4cf7fc604881fb9c27a32249bd071dd1eae20d66&token=868587677&lang=zh_CN#rd)
 > - [**听说你要绘制 scanpy 版的散点图?**](https://mp.weixin.qq.com/s?__biz=MzkyMTI1MTYxNA==&mid=2247509799&idx=1&sn=b3bc4bbbb8c1e3a98be3f5815cbcb4f0&chksm=c1849d56f6f3144000e22d4b9ebf989ad79349c450928c2a2346749b0187d857fca15d9e7183&token=613129250&lang=zh_CN#rd)