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ASHLEY

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GSE_file_GEO
GEOquery
autodock_vina_batch
chemmineR
clinical trails_drug
litsense_ncbi
radar_multiple_more
ocr
one_way_anova
regression-model
calculate_curve_rank
k-means cluster
heatmap_unique
ggraph_tree_network
ggraph
heatmap_line_point
mantel_test
One-Way ANOVA
unique combinations
k-mer_DNA
Bag of words BOW
DNA sequence RNA
fasttext
word2vec
One hot encoding 0 1
drugbank_website
ggsankey_ggplot2
ggimg_image_ggplot2
geom_text_repel
simple_bar_plot
geom_text_color_axis
webchem_example
point_line_Lollipop
ggplot2_ggnetwork
ggplot2_venn
wordcloud2
chromosome
T test in R for each row
pheatmap_simple_example
row sd
cut_break_y_axis
point_dot_error_bar
Overview of RCy3
pROC_threshhold
api_LitSense_ncbi
EOF within quoted string
duplicated_axis
lengend_order
3D-pie-chart_plotrix
updateR
Justify-angled-axis-text-on-top-axis
axis.text
Subscript superscript
Extract the legend
Spread_Gather_tidyr
DMwR_install_package
range_plot_ggforce_ggplot2
Sankey Diagram
https://app.rawgraphs.io/
T_Test-from-N_Mean_SD
Confidence Intervals _0.95
merge_dna_sequence
PCoA+PERMANOVA_pvalue
to_word_doc
Reconstruct symmetric matrix from values in long-form
df.long <- df.long[df.long$one != df.long$two,] df <- as.matrix(reshape::cast(df.long, one ~ two, fill=0) )
viability_data_tox21_code
rBLAST_package_sequence
Biostrings_dna_rna_aa
google-scholar_stat_plot
google-scholar
geom-step_ladder
pastel colors
funnel ggplot2
to-ppt-doc-export
Text-Mining_tm_package
ggplot2_circular_heatmap
Circular-heatmap-with-circlize-Plot-area-and-row-labels
col_mat[is.na(col_mat)] <- "gray90" dend <- set(dend_list,"branches_lty", 3)
world-cities-map
aggregrate
system.time: CPU Time Used
pubmed word cloud
ggtree_dendrogram_cluster
ggplot2_split_violin_half
ggsci_color_colour
network_code
parallel plot
KEGGREST
Human-Metabolome-Database
CTD_CHEM_GENE
chembl_dbi_package
http://ftp.ebi.ac.uk/pub/databases/chembl/ChEMBLdb/latest/
oncomineR_cancer_vs_normal
cgdsr_tcga
survival analysis
oncomineR
ggprism_code
bar_line_group_ggplot2
HEATMAP GGPLOT2
legend title position axis y text position
case_stringr
stratified sample
RF_VALIDATION
SVM_ROSE
ECFP4
over_circle-example
add table
overlap_circles_ggplot2
gap_ggplot
webchem_search
volcano_plot_ggplot2
circlize_plot
strReverse
pie_plot_ggplot2
compute_angle = function(perc){ angle = -1 #if(perc < 0.25) # 1st q [90,0] #angle = 90 - (perc/0.25) * 90 #else if(perc < 0.5) # 2nd quarter [0, -90] #angle = (perc-0.25) / 0.25 * -90 #else if(perc < 0.75) # 3rd q [90, 0] #angle = 90 - ((perc-0.5) / 0.25 * 90) #else if(perc < 1.00) # last q [0, -90] #angle = ((perc -0.75)/0.25) * -90 if(perc < 0.5) # 1st half [90, -90] angle = (180 - (perc/0.5) * 180) - 90 else # 2nd half [90, -90] angle = (90 - ((perc - 0.5)/0.5) * 180) return(angle) } sum_freq = sum(data_6$freq) secondLevel = data_6 %>% mutate(running=cumsum(freq), pos=running - freq/2) %>% group_by(1:n()) %>% mutate(angle=compute_angle((running - freq/2) / sum_freq)) p1 <- ggplot(data_6, aes(x = 1, weight = freq, fill = cancer)) + geom_bar(width = 1, colour = "black") + geom_text(x = 1.3, aes(y = centres, label = freq), colour = "black",size = 4) + scale_fill_manual(values=cancer_col,guide = leg) + #scale_fill_brewer(palette = c(), direction = -1, guide = leg) + #scale_color_brewer(palette = "black", direction = 1) + theme_minimal(base_family = "") + theme(legend.position = "", panel.grid.major = element_blank(), panel.grid.minor = element_blank(), axis.ticks = element_blank(), axis.text = element_blank(), axis.title = element_blank(), axis.line = element_blank()) + labs(fill = "", colour = "", caption = "") + ggtitle("", subtitle = "") + coord_polar(theta = "y",start = 0) #secondLevel$angle <- -abs(secondLevel$angle) p1 + geom_text(data=secondLevel, aes(label=paste(period), x=1.5, y=pos, angle=angle, hjust = c(rep(1, times=8),rep(0,times = 9))))
Edwards-Venn diagrams
venn_flower_plot
Arranging_plots_in_a_grid
cowplot
facet_wrap_line
pie_plot
radar_plot
flower
ref: https://mp.weixin.qq.com/s/cAZh-BOMUZH2YI1QQsgpkw
extract all table from PDF
#extract_text() converts the text of an entire file or specified pages into an R character vector. #split_pdf() and merge_pdfs() split and merge PDF documents, respectively. #extract_metadata() extracts PDF metadata as a list. #get_n_pages() determines the number of pages in a document. #get_page_dims() determines the width and height of each page in pt (the unit used by area and columns arguments). #make_thumbnails() converts specified pages of a PDF file to image files.
ridgeline_plot
combine_split_pdf_R
pheatmap_package
tiff(filename = paste0(dir_path,Sys.Date(),"-HP.tiff"),res = 300, width = 20, height = 20, units = "cm", pointsize = 12, compression = "lzw",bg = "white")
compare_PCA_PCoA_tSNE
venn_plot_R
upset_plot_cod
install.packages("UpSetR") library(UpSetR) movies <- read.csv( system.file("extdata", "movies.csv", package = "UpSetR"), header=TRUE, sep=";" ) data_1 <- movies[1:10,3:6] upset(data_1, nsets = 21, nintersects = 30, mb.ratio = c(0.5, 0.5), order.by = c("freq"), decreasing = c(TRUE))
Waffle charts in R
Dendrograms in R_ggplot2_cluster
cutree(hc, k = 2) # on hclust
msigdbr-package_for_gsea
PCA_PLOT
Calculates the Gini Impurity
Gini purity, a measure of clustering specificity. Gini purity of 1.0 would be perfect clustering by lineage.
calculating_Gini_coefficient
repel overlapping text labels
color_in_R
ROC-Curve
legend key backgroud
input_data_and_line_point_plot
Permutation and combination
Replace the first occurrence of a character
sub function
Michaelis-Menten model
Plotting means and error bars
legend detail
four-parameter log-logistic model
drc package modelFit(ryegrass.m1) -----> F value exp(e) -----> Inflection point
heatmap_ggplot2_axis_label
cgdsr_TCGA
STRINGdb_code
trim_plot
image_1 <- image_read_pdf(paste0(dir_path,dir_path_name[i]), pages = 1,density = 300)
GSEA_PLOT
Package fgsea version 1.14.0 sapply(data_5$leadingEdge, paste, collapse="/") ##################################################### data_3$log2.fold_change <- log2(data_3$FD) data_3$fcsign <- sign(data_3$log2.fold_change) data_3$logP=-log10(data_3$pvalue) data_3$metric= data_3$logP/data_3$fcsign #############################################################
treemap_ggplot2
heart plot
heatmap_ggplot2_revised
trycatch
Add gene annotation
heatmap_ggplot2